Are you running the same OS on both the laptop and your desktop? I doubt the computer is corrupting the download - I'd suggest that the first download may have been corrupt. Try wiping it out and downloading it again.
Read the Wiki: http://wiki.desmume.org/index.php?title=Faq#The_emulator_crashes_.2F_freezes
Did you try booting in Safe Mode and seeing if you can duplicate these issues?
As for Fallen Earth, all I could find was: http://forums.gamersfirst.com/topic/303071-need-help-game-crashes/
http://forums.gamersfirst.com/topic/299087-fallen-earth-does-not-launch-after-hi tting-launch/
Again - it's another beta, so stability issues and bugs are not uncommon.
It would seem that your issues are generally with free, beta software. On the whole, I would say these sorts of apps are far more likely to be buggy and problematic than *most* paid software - or free software that is supported by a paid development team (think Firefox and the like). Of course, we can all think of paid software that had more than a few bugs too!! At any rate, I don't think I'm going out on a limb by saying that there is nothing wrong with the new MBP - it's simply the software you're trying to run, none of which seems to be beyond the beta stage. I'm sure that's not the answer you were hoping for, but from here, that looks like the problem.