Hi John, I have to say that my rig is ultra high spec like the OP's rig and it is simply impossible that TRS12 is placing too many demands on the hardware. My GPU is watercooled and when I run TRS12 there is no discernible heat coming from the backplate but when running Far Cry 3 it still warms up but never crashes. The first time I ran a train in TRS12 my rig crashed totally and it destroyed Windows 7 so I had to do a fresh install. This is more than a glitch.
If a program crashes that hard enough to corrupt the operating system, then there's something wrong with the hardware. Seriously. My rig isn't much different than yours, except for the 680GTX and the water cooling which I don't have, and I've never seen anything like that. I see temps about 58C for my CPU continuously and no higher than 50C when using Trainz TS12 full graphics sliders and windowed while I'm browsing on my second monitor either on the forums, or watching YouTube videos.
What can cause that kind of problem?
Bad memory for one. I'd run MemTest86 and see what that has to say. The RAM today usually doesn't have error correction so there could be a flipped bit somewhere, or even marginally so enough, to cause data corruption.
I had a desktop many years ago that I could not install, then new, Windows NT 4.0 Workstation on. I would go through the process of installing only to have it crash as though the hard drive was faulty. In fact the message was something about a corrupted hard drive image. After trying a new hard drive, I went back to the place where I purchased the computer and the owner tried new memory which I didn't have. Problem solved in about 20 seconds. It was all about timing issues with the DIMMs. Memory issues can be troublesome to find because RAM can and will pass diagnostics, but will fail when put under stress.
Other issues too such as poor power from the mains will cause flaky problems. A poor ground, for example, can wreak havoc all over the place as it causes the logic levels to float ever so slightly. This floating can cause bits to change from a zero to a one and cause programs to crash and can cause data corruption. Speaking of power, a marginally working power supply can do this too. The problem is usually the +12V rail as this is split off for multiple uses. The +12 is used to drive the hard drives and is split up to +5 for other devices, and then that is split off to the lower values for RAM and motherboard components. If this rail is poorly regulated, then this can cause weird faults including data corruption which is caused by bad voltages driving both the memory and the hard drives.
So, given the history of data corruption, this is surely one area I'd look into as well.
John