The caps lock key state is virtualized. If you hit caps lock while in game, then alt+tab out and undo your caps lock, then it will be off outside, and on inside. I realize of course this is not desired behavior and that will be addressed at some point.
All you should have to do to fix it is the same thing you did to break it.
On the other hand, if it is SHIFT that is stuck, the fix is either to tap shift, or update to the current Inner Space.
In the future I would recommend posting Inner Space issues on the lavishsoft.com forums, and only post ISXVG (ISXEQ2, ISXEVE, etc) issues here, as this place is kind of its own little world and nobody seems to ask me what the real answer is to the questions that appear here, unless they think my code is causing a crash.