If I were to hazard a guess, the file format used by Pro Patches is an older version than what the audio library in Descent expects.
Have you tried it with the original patch set? I assume the game will just work fine with those (assuming a recent enough version).
In which case, the .PAT files might need to be 'upgraded' to a newer format.
I've found the PAT file documentation here: http://www.fileformat.info/mirror/corion/original.htm
It mentions a 12-character string at the start: 'GF1PATCH110'
Perhaps that version was updated at some point, and Descent expects a specific version, higher than what Pro Patches uses.
If you find some patches that do work, and they have a higher number in that string, you could try just editing the BELLTREE.PAT file to see if it goes through. If so, then you can probably fix all of them that way.
Edit: I've downloaded the latest GUS disks and checked, they have GF1PATCH110 as well.
So it may not be the version string that's the issue, but it might also check other info, such as the application name or ID. You could try copying that from the working patches into the Pro Patches, to see if it makes a difference.