I have the same sort of issue... It's really becoming a hassle. I get a text, tap to open the message, slide open the keyboard right after...

If I start typing, the contacts application will open and intercept all my keystrokes. If I wait, sometimes it will just close the messaging application and go back to landscape TF3D.

Removed my custom HTCVolumeControl.dll and soft reset, the stock one loaded back in... Same problem. So I just replaced it. This is really a PITA at this point.