In short, no there's nothing you can do about this issue. It's a common problem that has been discussed many, many times before and by not addressing it the developers have indicated it's not a priority for them.
The good thing is that it appears to be simply a nuisance. The shutdown doesn't corrupt your file or lose any data. You just have to start it up again. It is somewhat dependent on other programs running in the background. Shut down everything you don't need. I've found that even running Media Player and listening to music is too much for FTM.