In the structure of your VI's, be certain that you are not repetively creating things such as references to queues, or file references, or DAQ tasks, or anything without closing them. I was working on one application where a DAQ task was getting created every loop iteration and not being closed. It crashed the PC hard with a blue screen of death after about 20 minutes of operation, through debugging and before I found the cause, I saw I had about 80,000 to 100,000 iterations of a loop fairly consistently before the crash.
If this loop had run at a slower rate, it might have taken days or weeks before the PC would have crashed. It would have seemed infrequent and would have taken longer to debug because I would never have seent the pattern. If it takes a few failures before you discover the problem, it is a lot quicker to find the explanation after a few failures at 20 minutes per failure as opposed to 20 days per failure. The problem was eventually found in a subVI several layers down and fixed.
So if you pay attention to these things early enough, then hopefully they won't pop up and bite you weeks or months into a critical run of the program.
