My Save Game not working in GOG version.

Whoah, too much information dude.

Try installing the game outside the Program Files folder, somewhere like X:\GOG Games\Quake 2. Then copy your save files there and see if it works.

How do we know the saves are compatible? Is it even worth the hassle? The game is not that long.

Same problem.

Sounds like differing versions may be the cause. My guess is that GOG's version is fully patched while you didn't apply all (if any) official patches to your CD version you created those saved games on. If that's the case there's probably nothing you can really do about it except starting over. Also this.

Are you sure you're copying it to the correct folder. There is a possibility that GOG's version might be saving them elsewhere. There was something similar with Populous 3 if I remeber correctly. It's worth checking.

Load up GOG's version. Make a save. Check where the file is located.

Indeed, but AFAIK it's only an issue if you install in Program Files (and don't automatically run everything as administrator). Neither the installers nor Galaxy use Program Files as the default directory any more, though.

Honestly, it would be better to just start the game over. When Quake 2 was first released in 1997, id Software kept releasing patch after patch, and each new patch would invalidate the saves of the previous patch. I would recommend using the latest v3.24 patch for Quake 2 and then start a new game.