When you say they won't launch you mean when you click on them in Steam nothing happens? How do you know it's .NET? A lot of my games have that pop up everytime you launch saying installing .NET for first time use, but the game still launches afterwards. I've always seen that pop-up on certain games, and I recall reading that's common/no problem.
Can you be specific what games you're having issues with, and how exactly they aren't "launching"?
An interesting issue developed for me about a month ago where most of my games won't play, on a bottle I had been using for a long time. For instance Portal 2, crashes right where it'd get to the main menu part, CS:S the same, Civ5 crashes when you try to play a game, etc. I'm fairly certain the issue is nvidia-drivers.. There's been numerous memory bugs with anything over 319.30 (i believe), and I know i tried 319.76, 325.15, and 331.20 and all versions would fail to launch/play many of my games. Downgraded to 304.117 and it works. May not be your problem, but figured I'd mention.