Here are my Direct rips from the retail disks and the Cue's used on them. A few renames per file EG:
FILE "WINQUAKE.BIN" BINARY to: FILE "game.gog" BINARY
FILE "ARMAGON.BIN" BINARY to: FILE "gamea.gog" BINARY
FILE "DISSOLUTION.BIN" BINARY to: FILE "gamed.gog" BINARY
After the renames cut and past track into into the respective *.CUE files in the //Quake directory. Hope this helps anyone with there copies. Sorry, i should have tested i thought it would work :/

Have you verified that the retail discs identical to the GOG images?

Thanks for the effort but this pretty much confirmed that the retail discs and the GOG versions are slightly different. I tried your .cues and what ended up happening was all the music was completely off.

I own several disc-based versions of Quake, but none of them seem to match the image files in the GOG release. So either they (GOG) did something to the contents themselves, or the discs that came in the Offering box (which I don't have, but seems to be the source for this release) were altered from most other releases of the game. I can't imagine why, though.

Regardless of what caused it, it is most irritating that currently the only digital release of the game with soundtrack included has this "bug".

They just need to rerip the disks to create new .cue would take all of 15 minutes. here is the version GOG has and incorrectly ripped images from. Quake the Offering from Activision

I thought someone already made the fixed .cue sheet manually, am I wrong?

I cant find one, they basically said reduce by 2 minutes and it "should" work but the tracks are slightly off still.

*seconds*, not minutes. Otherwise the tracks will be more than "slightly off". :-)

Look here: https://www.gog.com/forum/quake_series/quake_the_offering_incorrect_cue_sheets