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I loved this game as a young trek fan and am ecstatic that it and others have finally come to gog but after installing it I noticed upon my first play-through that sometimes the audio is a bit choppy or pops slightly, any idea why this might be and what I can do to remedy the situation?
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In the DOSBox config file, check if the cycle speed is set to max.

If so, change it to

fixed 10000

That should work fine for a VGA 386 era game.

If the game feels a bit slow, try 15000 or 20000.

I'm not sure why GOG keeps using cycle max, this is known to bug out any game with speed sensitivity issues.