I am not a veteren at this, and as such, I do not know which features where added when or what toolboxes they are part of.
When I right-click to bring up a the function menu, inside "Structures" there is an options for "Timed Loop". It looks like a while loop, but blue and with a little tab on the left of it. You can reference a timebase in it and it might give you more control over how your loop runs. If you don't have it, then my idea is of little help. Perhaps you can experiment with the different between the "Wait (ms)" and "Wait until next Millisecond" blocks and see if one might perform better for you than another. With software timed applications like yours, other processing threads (other programs running on the computer) can play havoc with LV's priority. If it is feasible, it might behoove you to try it after a fresh reboot, with as many other applications closed as possible.
Best of luck with your problem, I am sorry I could not be of more help.