I think your VI needs a serious redesign. I don't think it will ever work like that.
There is no data dependency between the last two while loops and the construct of 5 while loops on the left so they'll all run in parallel. Most likely, the USB port will be closed by the last loop while it is still being used inside the loops on the left. A "wait(ms)" and a "wait until next ms multiple" next to each other in the same loop also seems quite odd (third loop).
The first loop spins millions of times a second just to see if a button is pressed. You could use an event structure instead or at least place a small wait in that loop. Right no it spins so fast that it consumes all CPU, starving all other running processes.
Could you also point out in which loop you want to measure the time?