"Is there any precaution that I should take to use this VI."
Yes many,
When you start to experiment with settings priorities in an attempt to avoid the affects of mouse clicks, then you should brace yourself for the application appearing hung. This would happen if LV had a higher priority than the mouse interupt service routine.
Same applies to the other conditions you mentioned.
If you go this route, backup before you experiment! Some strange things can happen to your file system.
I have talked to you about this challenge of yours in another thread. This is what I recomend.
1) If you can live with your readings being made on only one gear at a time, AND the sample rate being aperiodic, then you MAY be able to use DAQ Occurances and two session. I
have not done this myself, and AM NOT SURE if it can be done or if you hardare supports it, but maybe;
a) Open two references to your and configure A so it uses hardware timing (like you already said works good) to count gear A using the other counter as the gate. On the other session you are counting gear B.
b) Configure both of the above to fire occurances when done.
c)Start only session A.
d) When A occurance fires start B.
e) When B fires start A, etc.
This will give you determinism on the counts and effectively shift the indeterminism to the update interval.
If this is not good enough then there is another option. Can you get yourself a nice solid external reference that you can apply as an external gate to both counters? If so you will be using hardware timing and you should be on the right track.
If these do not work out, you may end up having to go to different hardware.
Just trying to help,
Ben