Index: firmware/App/Controllers/BloodLeak.c
===================================================================
diff -u -r2c1c34c153a146d659976b3aa499937b88264b1b -r1145e9197855b4f2cb79eb407d3899059b0ca410
--- firmware/App/Controllers/BloodLeak.c	(.../BloodLeak.c)	(revision 2c1c34c153a146d659976b3aa499937b88264b1b)
+++ firmware/App/Controllers/BloodLeak.c	(.../BloodLeak.c)	(revision 1145e9197855b4f2cb79eb407d3899059b0ca410)
@@ -89,6 +89,7 @@
 #define BLOOD_LEAK_EMB_MODE_NUM_OF_INFO_CMDS  3                                                  ///< Blood leak embedded mode number of informative commands.
 
 #define BLOOD_LEAK_FPGA_ERROR_TIMEOUT_MS     ( 2 * MS_PER_SECOND )                               ///< Blood leak embedded mode FPGA error timeout in milliseconds.
+#define BLOOD_LEAK_RXFIFO_COUNT_MASK         0x03ff                                              ///< Mask high order bits of blood leak sensor rx count
 
 /// Defined states for the blood leak detector state machine.
 typedef enum BloodLeakStates
@@ -198,6 +199,7 @@
 static BOOL isEmbModeCmdQueueEmpty( void );
 static U32 getAvailableEmbModeQueueCount( void );
 static void enqueueInfoEmbModeCmds( void );
+static U16 getBloodLeakRxBytesAvailable( void );
 
 /*********************************************************************//**
  * @brief
@@ -368,6 +370,9 @@
         enqueueEmbModeCmd( Z_EMB_MODE_CMD );
         enqueueEmbModeCmd( Q_EMB_MODE_CMD );
         enqueueEmbModeCmd( T_EMB_MODE_CMD );
+
+        // Since the zero commands have been queued, reset the counter
+        bloodLeakEmbModeCmdEnqueueCount = 0;
     }
     else if ( ++bloodLeakEmbModeCmdEnqueueCount > BLOOD_LEAK_EMB_MODE_MAX_NUM_CMD_TRIES )
     {
@@ -895,7 +900,7 @@
     if ( ( bloodLeakEmbModeRqstedCmd != CS_EMB_MODE_CMD ) && ( bloodLeakUARTCmdIndex - 1 > BLOOD_LEAK_EMB_MODE_RESET_INDEX ) &&
          ( bloodLeakUARTCmdIndex - 1 <= BLOOD_LEAK_EMB_MODE_RESET_INDEX + 1 ) )
     {
-        if ( BLOOD_LEAK_EMB_MODE_RX_BUFFER_EMPTY == getFPGABloodLeakRxFIFOCount() )
+        if ( 0 == getBloodLeakRxBytesAvailable() )
         {
             // TODO do nothing right now. I case it was decided to use the terminal mode again, make sure the reset went through prior to sending the
             // reset of the command sequence
@@ -941,7 +946,7 @@
 static BLOOD_LEAK_EMB_MODE_STATE_T handleBloodLeakEmbModeWaitForCommandResponseState( void )
 {
     BLOOD_LEAK_EMB_MODE_STATE_T state = BLOOD_LEAK_EMB_MODE_WAIT_FOR_COMMAND_RESPONSE_STATE;
-    U08 rxFIFOCount                   = getFPGABloodLeakRxFIFOCount();
+    U16  rxFIFOCount                  = getBloodLeakRxBytesAvailable();
     BOOL hasCharBeenReceived          = FALSE;
     U32 commandTimeoutMS              = bloodLeakEmbModeCmd[ bloodLeakEmbModeRqstedCmd ].timeoutMS;
     U32 length                        = bloodLeakEmbModeCmd[ bloodLeakEmbModeRqstedCmd ].length;
@@ -1635,4 +1640,9 @@
     return result;
 }
 
+static U16 getBloodLeakRxBytesAvailable( void )
+{
+    return getFPGABloodLeakRxFIFOCount() & BLOOD_LEAK_RXFIFO_COUNT_MASK;
+}
+
 /**@}*/