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While the DOS edition has it's flaws about framerate its more consistent then the new Windows version that was released. The audio cd change options has no affect on the windows version.

Just tested it for the first time, not impressed.

My monitor also freaked out while the Windows version was checking for available resolutions and crashed a couple of times.
hockeycanuck, have you fixed this problem yet?

I had exactly the same problem when I tried the Windows version from GOG. I do not want to use the DOS version because the ball movement is kind of choppy. The choppiness is subtle but it is there - I think that's because of DOSBox and not because of the Timeshock! version itself.
Aside from the music problem in the Windows version I also had the strange behaviour of all ball movements being in slow motion (completely smooth but at 1/2 or 1/4 of the original game's speed).
I tried everything to get these problems solved but unfortunately was not able to do so - at least not with the GOG version of the game.

I got an old Windows version (1.08) off ebay (a game compilation cd without the cd audio tracks) and it worked like a charm out of the box. I then mounted the GOG image with Daemon Tools and the ebay version detected the audio tracks correctly. I can finally play without any problems.

Maybe this could be the way for you, too?