It wouldnt surprise me if there are many more hidden game protection systems than the couple the devs responded to.
I'm using the Disk (unfortunately), so I can only assume that my bugs are bugs, and there are a lot. Though I have heard of people with Nforce 3/4 boards getting false positives when it comes to protection due to the protection systems being unable to detect the controller properly on those boards, but this was a couple year back. I have no idea what its like now.
I had a crash during gameplay, and my saves would not reload from that mission. Though up until the crash they were loading fine. That is as close as I have got to your problem. I'm on my second boat now.
Im having the same bugs as everyone else.
http://www.subsim.com/radioroom/showthread.php?t=107766