So when I came in this morning and checked the machine, it was frozen just like normal. There was also a dialog box from NISpy saying that it had encountered an error writing the log file. It seems that NISpy still has a 2GB file limit in it, since the size of the capture file is exactly 2^31 - 1 bytes. I was quite surprised by that as I had thought that that problem had been taken care of a while ago, but then again National Instruments does seem to have a few issues with keeping software up to date.
Anyways, things are still the same after the few changes I made to keep the serial port open all the time (thanks for that though, it was still a good thing to do). I had wondered if it was caused by another program trying to access the serial port at the same time, but I cant think of anything else that would be doing that and fuser shows that LabView is the only process that has the serial port open. Im really at a loss as to what this could be.