706 had the curse of all curses

[DonRotolo]

My condolences.

We had a similar issue, seen in practice and competition. We were fortunate to have Greg from NI at the NJ regional take a close look at things, and his conclusion was that our software was overtaxing the cRio. That is, when we kept the cRio too busy, after a while it eventually had to stop and do some housekeeping, which is when the outputs dropped (exactly what you are seeing).

To help solve this, we removed all unnecessary code (like the vision processing and several debugging routines). We're now examining our PID loops to make sure they are running at reasonable rates (perhaps 10 Hz instead of the max the CPU can support). We're also checking all conditionals and wait states,since while we force the cRio to wait it can't do ANYthing...

Perhaps a careful review of your code may be of value.