I thought this issue that was brought up on the Steam version of Twinkle Star Sprites was fixed and would be here for the GOG.com release, but it seems like there is a heavy amount frame-skipping which also desyncs the audio of the game and I'm not referring to the slowdowns that also happens in the original arcade version of the game. I assume the original arcade version of the game ran at 60 FPS, but it seems that this version of the game is going above 60 a lot and all over the place, running between 80-110+ FPS and the game can't handle that since it wasn't designed for very high frame-rates. I have tried various methods of trying to cap the frame-rate, from forcing V-sync using Nvidia control panel and D3DOverrider, and trying to force the game's frame-rate to 60 FPS with Nvidia Profile Inspector to no avail.

I have no idea if TSS has been updated (on Steam) since I activated and played it on Steam (that was when Humble sold a SNK games bundle, dec. 2015 I think), but back then the game played at about the right speed and with the right amount of slowdown for me (I didn't compare arcade and Steam face-to-face, but have played the arcade release with MAME enough that I would spot any obvious difference like what you are describing) :/

If you are on a 120Hz (or higher) monitor, that might be the culprit, as some programs behave bad with those - they force V-sync but as their logic is tied to the framerate and they actually expect a 60Hz refresh rate, they end up running at twice the normal speed.

The following video is recorded from actual MVS hardware: https://www.youtube.com/watch?v=VPKVc5m6Su4. Your game should definitely run in a similar fashion.

Thing is my HDTV that I'm using on my computer is 60 Hz.