Okay, first of all, thanks to the developers for replying! That means a great deal to me and it shows me that you take all of us seriously or at least trying to do so. Thanks indeed!
Now the answer to the questions you asked: I run my STO in full screen mode, always. I tried the software cursor option several times, it didn't change a thing. I apologize for the register thing on the forum I've posted my DX-Diag, I'll split it up and post it again in here, probably will take 3 or 4 posts in a row then, I hope that's okay with you guys.
About the windowed mode solution (moving the mouse outside of the game area): I can tell you from experience that after I had to exit the game due to extensive mouse lag (it's only the cursor, the game itself never lags), the mouse kept lagging in my OS for about one or two mintues, but after that, everything was back to normal every time I had to exit the game.
Now the DX-Diag that was being asked for. Sorry it took me a bit longer to reply this time: