What sort of CPU utilization are you seeing on your cRio when the issue is occurring?
This year, while I was away some of our students encountered an issue where one of our periodic loops was overrunning the amount of time we had allotted for it, just slightly. They lost a lot of hair trying to determine why ghost problems seemed to just be appearing and disappearing uncorrelated to the changes they were making, turned out to be that after about 6 minutes of on time, the overrun would result in our cRio not having any CPU time left to perform its other tasks, and seemingly ghost like issues would appear, with solenoids moving in and out and lag and inconsistent behavior on multiple subsystems.
Correcting the loop naturally resolved the issue. For the record, the acquire or create semaphore reference VI is not the fastest thing in the world, and you should save semaphore references, rather than fetch them with it, if they're going to be used heavily.
