Index: firmware/App/Controllers/BloodFlow.c
===================================================================
diff -u -r4a41a54d255afc5cef0599e2a832927ed2b0ee5d -r22f7bcd7e26dc6be337fdb6adbc9281e8f60dbbc
--- firmware/App/Controllers/BloodFlow.c	(.../BloodFlow.c)	(revision 4a41a54d255afc5cef0599e2a832927ed2b0ee5d)
+++ firmware/App/Controllers/BloodFlow.c	(.../BloodFlow.c)	(revision 22f7bcd7e26dc6be337fdb6adbc9281e8f60dbbc)
@@ -341,12 +341,10 @@
     {
         // set initial PWM duty cycle
         bloodPumpPWMDutyCyclePctSet = BP_PWM_ZERO_OFFSET + MAX_BLOOD_PUMP_PWM_STEP_CHANGE;
-        etpwmSetCmpA( etpwmREG1, (U32)FLOAT_TO_INT_WITH_ROUND( bloodPumpPWMDutyCyclePctSet * (F32)(etpwmREG1->TBPRD) ) );
+        etpwmSetCmpA( etpwmREG1, (U32)( (S32)( ( bloodPumpPWMDutyCyclePctSet * (F32)(etpwmREG1->TBPRD) ) + FLOAT_TO_INT_ROUNDUP_OFFSET ) ) );
         // allow blood pump to run in requested direction
         setBloodPumpDirection( bloodPumpDirection );
         releaseBloodPumpStop();
-        // start PWM for blood pump
-        etpwmStartTBCLK();
         isBloodPumpOn = TRUE;
         result = BLOOD_PUMP_RAMPING_UP_STATE;
     }
@@ -373,7 +371,7 @@
     {
         // start ramp down to stop
         bloodPumpPWMDutyCyclePctSet -= MAX_BLOOD_PUMP_PWM_STEP_CHANGE;
-        etpwmSetCmpA( etpwmREG1, (U32)FLOAT_TO_INT_WITH_ROUND( bloodPumpPWMDutyCyclePctSet * (F32)(etpwmREG1->TBPRD) ) );
+        etpwmSetCmpA( etpwmREG1, (U32)( (S32)( ( bloodPumpPWMDutyCyclePctSet * (F32)(etpwmREG1->TBPRD) ) + FLOAT_TO_INT_ROUNDUP_OFFSET ) ) );
         result = BLOOD_PUMP_RAMPING_DOWN_STATE;
     }
     // have we reached end of ramp up?
@@ -387,7 +385,7 @@
     else
     {
         bloodPumpPWMDutyCyclePctSet += MAX_BLOOD_PUMP_PWM_STEP_CHANGE;
-        etpwmSetCmpA( etpwmREG1, (U32)FLOAT_TO_INT_WITH_ROUND( bloodPumpPWMDutyCyclePctSet * (F32)(etpwmREG1->TBPRD) ) );
+        etpwmSetCmpA( etpwmREG1, (U32)( (S32)( ( bloodPumpPWMDutyCyclePctSet * (F32)(etpwmREG1->TBPRD) ) + FLOAT_TO_INT_ROUNDUP_OFFSET ) ) );
     }
 
     return result;
@@ -424,7 +422,7 @@
     else
     {
         bloodPumpPWMDutyCyclePctSet -= MAX_BLOOD_PUMP_PWM_STEP_CHANGE;
-        etpwmSetCmpA( etpwmREG1, (U32)FLOAT_TO_INT_WITH_ROUND( bloodPumpPWMDutyCyclePctSet * (F32)(etpwmREG1->TBPRD) ) );
+        etpwmSetCmpA( etpwmREG1, (U32)( (S32)( ( bloodPumpPWMDutyCyclePctSet * (F32)(etpwmREG1->TBPRD) ) + FLOAT_TO_INT_ROUNDUP_OFFSET ) ) );
     }
 
     return result;
@@ -452,7 +450,7 @@
     {
         newPWM = runPIController( PI_CONTROLLER_ID_BLOOD_FLOW, tgtFlow, actFlow );
         bloodPumpPWMDutyCyclePctSet = newPWM;
-        etpwmSetCmpA( etpwmREG1, (U32)FLOAT_TO_INT_WITH_ROUND( bloodPumpPWMDutyCyclePctSet * (F32)(etpwmREG1->TBPRD) ) );
+        etpwmSetCmpA( etpwmREG1, (U32)( (S32)( ( bloodPumpPWMDutyCyclePctSet * (F32)(etpwmREG1->TBPRD) ) + FLOAT_TO_INT_ROUNDUP_OFFSET ) ) );
         bpControlTimerCounter = 0;
     }
 
@@ -473,7 +471,6 @@
     isBloodPumpOn = FALSE;
     bloodPumpPWMDutyCyclePctSet = 0.0;
     etpwmSetCmpA( etpwmREG1, 0 );
-    etpwmStopTBCLK();
     SET_BP_STOP();
 }
 
@@ -656,6 +653,7 @@
     flowReadingsTotal = 0.0;
     flowReadingsIdx = 0;
     flowReadingsCount = 0;
+    flowReadingsTmrCtr = 0;
     bpControlTimerCounter = 0;
 }
 
@@ -711,7 +709,7 @@
                 break;
 
             default:
-                // TODO - s/w fault?
+                SET_ALARM_WITH_2_U32_DATA( ALARM_ID_SOFTWARE_FAULT, SW_FAULT_ID_BLOOD_FLOW_INVALID_FILTER_STATE, flowReadingsTmrCtr )
                 break;
         }
     }
Index: firmware/App/Controllers/DialInFlow.c
===================================================================
diff -u -r4a41a54d255afc5cef0599e2a832927ed2b0ee5d -r22f7bcd7e26dc6be337fdb6adbc9281e8f60dbbc
--- firmware/App/Controllers/DialInFlow.c	(.../DialInFlow.c)	(revision 4a41a54d255afc5cef0599e2a832927ed2b0ee5d)
+++ firmware/App/Controllers/DialInFlow.c	(.../DialInFlow.c)	(revision 22f7bcd7e26dc6be337fdb6adbc9281e8f60dbbc)
@@ -40,7 +40,7 @@
 #define MAX_DIAL_IN_FLOW_RATE                 500             // mL/min
 #define MIN_DIAL_IN_FLOW_RATE                 100             // mL/min
 
-#define MAX_DIAL_IN_PUMP_PWM_STEP_CHANGE      0.02            // duty cycle    TODO - fixed or parameterized or set in motor controller?
+#define MAX_DIAL_IN_PUMP_PWM_STEP_CHANGE      0.005           // duty cycle    TODO - fixed or parameterized or set in motor controller?
 #define MAX_DIAL_IN_PUMP_PWM_DUTY_CYCLE       0.88            // controller will error if PWM duty cycle > 90%, so set max to 88%
 #define MIN_DIAL_IN_PUMP_PWM_DUTY_CYCLE       0.12            // controller will error if PWM duty cycle < 10%, so set min to 12%
 
@@ -341,13 +341,11 @@
     if ( getTargetDialInFlowRate() != 0 )
     {
         // set initial PWM duty cycle
-        dialInPumpPWMDutyCyclePctSet = MAX_DIAL_IN_PUMP_PWM_STEP_CHANGE;
-        etpwmSetCmpA( etpwmREG1, (U32)FLOAT_TO_INT_WITH_ROUND( dialInPumpPWMDutyCyclePctSet * (F32)(etpwmREG1->TBPRD) ) );
+        dialInPumpPWMDutyCyclePctSet = DIP_PWM_ZERO_OFFSET + MAX_DIAL_IN_PUMP_PWM_STEP_CHANGE;
+        etpwmSetCmpA( etpwmREG2, (U32)( (S32)( ( dialInPumpPWMDutyCyclePctSet * (F32)(etpwmREG2->TBPRD) ) + FLOAT_TO_INT_ROUNDUP_OFFSET ) ) );
         // allow dialIn pump to run in requested direction
         setDialInPumpDirection( dialInPumpDirection );
         releaseDialInPumpStop();
-        // start PWM for dialIn pump
-        etpwmStartTBCLK();
         isDialInPumpOn = TRUE;
         result = DIAL_IN_PUMP_RAMPING_UP_STATE;
     }
@@ -374,7 +372,7 @@
     {
         // start ramp down to stop
         dialInPumpPWMDutyCyclePctSet -= MAX_DIAL_IN_PUMP_PWM_STEP_CHANGE;
-        etpwmSetCmpA( etpwmREG1, (U32)FLOAT_TO_INT_WITH_ROUND( dialInPumpPWMDutyCyclePctSet * (F32)(etpwmREG1->TBPRD) ) );
+        etpwmSetCmpA( etpwmREG2, (U32)( (S32)( ( dialInPumpPWMDutyCyclePctSet * (F32)(etpwmREG2->TBPRD) ) + FLOAT_TO_INT_ROUNDUP_OFFSET ) ) );
         result = DIAL_IN_PUMP_RAMPING_DOWN_STATE;
     }
     // have we reached end of ramp up?
@@ -388,7 +386,7 @@
     else
     {
         dialInPumpPWMDutyCyclePctSet += MAX_DIAL_IN_PUMP_PWM_STEP_CHANGE;
-        etpwmSetCmpA( etpwmREG1, (U32)FLOAT_TO_INT_WITH_ROUND( dialInPumpPWMDutyCyclePctSet * (F32)(etpwmREG1->TBPRD) ) );
+        etpwmSetCmpA( etpwmREG2, (U32)( (S32)( ( dialInPumpPWMDutyCyclePctSet * (F32)(etpwmREG2->TBPRD) ) + FLOAT_TO_INT_ROUNDUP_OFFSET ) ) );
     }
 
     return result;
@@ -425,7 +423,7 @@
     else
     {
         dialInPumpPWMDutyCyclePctSet -= MAX_DIAL_IN_PUMP_PWM_STEP_CHANGE;
-        etpwmSetCmpA( etpwmREG1, (U32)FLOAT_TO_INT_WITH_ROUND( dialInPumpPWMDutyCyclePctSet * (F32)(etpwmREG1->TBPRD) ) );
+        etpwmSetCmpA( etpwmREG2, (U32)( (S32)( ( dialInPumpPWMDutyCyclePctSet * (F32)(etpwmREG2->TBPRD) ) + FLOAT_TO_INT_ROUNDUP_OFFSET ) ) );
     }
 
     return result;
@@ -453,7 +451,7 @@
     {
         newPWM = runPIController( PI_CONTROLLER_ID_DIALYSATE_FLOW, tgtFlow, actFlow );
         dialInPumpPWMDutyCyclePctSet = newPWM;
-        etpwmSetCmpA( etpwmREG1, (U32)FLOAT_TO_INT_WITH_ROUND( dialInPumpPWMDutyCyclePctSet * (F32)(etpwmREG1->TBPRD) ) );
+        etpwmSetCmpA( etpwmREG2, (U32)( (S32)( ( dialInPumpPWMDutyCyclePctSet * (F32)(etpwmREG2->TBPRD) ) + FLOAT_TO_INT_ROUNDUP_OFFSET ) ) );
         dipControlTimerCounter = 0;
     }
 
@@ -473,8 +471,7 @@
 {
     isDialInPumpOn = FALSE;
     dialInPumpPWMDutyCyclePctSet = 0.0;
-    etpwmSetCmpA( etpwmREG1, 0 );
-    etpwmStopTBCLK();
+    etpwmSetCmpA( etpwmREG2, 0 );
     SET_DIP_STOP();
 }
 
@@ -656,6 +653,7 @@
     flowReadingsTotal = 0.0;
     flowReadingsIdx = 0;
     flowReadingsCount = 0;
+    flowReadingsTmrCtr = 0;
     dipControlTimerCounter = 0;
 }
 
@@ -711,7 +709,7 @@
                 break;
 
             default:
-                // TODO - s/w fault?
+                SET_ALARM_WITH_2_U32_DATA( ALARM_ID_SOFTWARE_FAULT, SW_FAULT_ID_DIAL_IN_FLOW_INVALID_FILTER_STATE, flowReadingsTmrCtr )
                 break;
         }
     }
Index: firmware/App/Services/AlarmMgmt.h
===================================================================
diff -u -r07b9515c080aa68fecfa331cbc593adea4c0b8dc -r22f7bcd7e26dc6be337fdb6adbc9281e8f60dbbc
--- firmware/App/Services/AlarmMgmt.h	(.../AlarmMgmt.h)	(revision 07b9515c080aa68fecfa331cbc593adea4c0b8dc)
+++ firmware/App/Services/AlarmMgmt.h	(.../AlarmMgmt.h)	(revision 22f7bcd7e26dc6be337fdb6adbc9281e8f60dbbc)
@@ -163,6 +163,8 @@
     SW_FAULT_ID_DIAL_OUT_FLOW_INVALID_DIAL_OUT_PUMP_DIRECTION,
     SW_FAULT_ID_DIAL_OUT_FLOW_INVALID_DIAL_OUT_PUMP_STATE,
     SW_FAULT_ID_DIAL_OUT_FLOW_SET_TOO_HIGH,
+    SW_FAULT_ID_BLOOD_FLOW_INVALID_FILTER_STATE,
+    SW_FAULT_ID_DIAL_IN_FLOW_INVALID_FILTER_STATE,                      // 45
     NUM_OF_SW_FAULT_IDS
 } SW_FAULT_ID_T;
 
Index: firmware/source/sys_main.c
===================================================================
diff -u -r4a41a54d255afc5cef0599e2a832927ed2b0ee5d -r22f7bcd7e26dc6be337fdb6adbc9281e8f60dbbc
--- firmware/source/sys_main.c	(.../sys_main.c)	(revision 4a41a54d255afc5cef0599e2a832927ed2b0ee5d)
+++ firmware/source/sys_main.c	(.../sys_main.c)	(revision 22f7bcd7e26dc6be337fdb6adbc9281e8f60dbbc)
@@ -131,6 +131,13 @@
     adcInit();      // configure internal ADC channels
     mibspiInit();   // re-purposing MIBSPI5 I/O/C pins as GPIO
     etpwmInit();    // configure PWMs
+        etpwmSetCmpA( etpwmREG1, 0 );
+        etpwmSetCmpA( etpwmREG2, 0 );
+        etpwmSetCmpA( etpwmREG3, 0 );
+        etpwmSetCmpA( etpwmREG4, 0 );
+        etpwmSetCmpA( etpwmREG6, 0 );
+        etpwmSetCmpA( etpwmREG7, 0 );
+        etpwmStartTBCLK();
     canInit();      // CAN1 = CAN, re-purposing CAN2 and CAN3 Rx and Tx pins as GPIO
         //canEnableloopback( canREG1, External_Lbk );  // TODO - debug code
     sciInit();      // SCI1 used for PC serial interface, SCI2 used for FPGA serial interface