I just downloaded a copy of Pegasus Prime from GOG, it was labeled as being compatible with Windows 10 but I'm getting the exact same problem I had with my physical copy I bought years back when it first became available.

The video lags a great deal, and when an FMV is playing it not only lags but also makes the audio slightly choppy in places.

I know I had to make some adjustments to the game settings to get it to run in Windows 7 back before I 'upgraded' to Windows 10 (if you want to even call it an upgrade, outside of easier-to-manage protections against viruses and malware I'm not all that impressed with the OS but I can't exactly do anything about that at the moment).

Does anyone have a solution (OS is 64 bit, x64 configuration)? I'd hate to think I wasted money on another copy of a game I've been jonesing to play for the past 5 years (and already had to wait over 10 just to get a Windows-compatible version)...

Sorry for the delay in getting back to you. What is your hardware configuration?

Configuration:

Windows 10 Home, x64-based.

What other info do you need?

If you have a large monitor, the system may by trying to scale the original screen size to fit without hardware support. Look for the Pegasus Prime program file and select properties, the try running in it compatibility mode and/or check "Run in 640 x 480 screen resolution" (if available).

The link below has some more recommendations that can help:
http://thejourneymanproject.com/presto/journeymanprime/support.html