Data acquisition/control is reduced when reading in frequency

Question

I am using a 6024E interface to operate a PID loop that keeps the RPM stable of a servomotor but having problems when attempting to read frequency at the same time from a flow-meter.
Basically the operation of the system is as follows;-
User sets an RPM demand, say 5000RPM, an analog signal is sent out to the motor controller which equates to this RPM (obtained operating system open loop) and motor runs up to this value after a brief delay. The feedback from the motor is from its shaft encoder which gives 1000 PPR, after signal conditioning in hardware this signal is applied to the gate of timer 0 and after scaling applied to the PID loop. This configuration is now quite stable and responds quite well to the operator demands. However the first problem was noticed when the RPM demand was taken to zero and an attempt to halt the program was made. There was a delay in shutting down that was roughly equiv to the time out value which was set on the DAQMX read Vi.
Things became much worse when a further loop was added to read a flowmeters frequency output (approx 50 to 300Hz max, counter 1) that varied with the servo motors RPM demand. This additional routine has almost stopped the whole program initially starting as it appears that counter channel 1 is waiting for an input before letting the rest of the program run. I have tried using the trigger functions to control the counters, i.e disable them until the servo motor reaches say 1000RPM but keep getting errors to say that mode is not supported. I guess that I could probably call the whole routine for the frequency measument only when required by using a case statement, but this seems to be a bit 'rough', configuring channels, start, read, stop etc every time the frequency needs to be read. The flow meter reading, once running needs to be fairly accurate because this will ultimatly be used in anoither closed loop to operate a stepper motor that controls the fluid flow through the flowmeter.
Sorry the above is a bit long winded and there is probably a really simple solution to controlling the counter inputs but I think I have tried most of the examples and previous suggestions that I could find on the forum. Also is there any way I could sync the analog output signal to the counter freq read signal? I found examples in the help files for this but using 'count edges' not frequency or period mode.
Thanks John
Labview Version 8.5
Labview Version 8.6
Labview Version 2013

Answer 1

Question re-posted in Labview forum with the Frequency read vi that is being used 
Labview Version 8.5
Labview Version 8.6
Labview Version 2013