Ok, I think it does actually have something to do with this.
Try the following (with an uncorrupted KQ6-CD, lol):
- File->Import Patch File, and choose the 65535.map in the KQ6 directory
- Give it resource number 65535 and click ok to import
- Close the game
- Delete 65535.map from the KQ6 directory (or rename it to something else so neither Companion or Sierra.exe will find it)
- Re-open the game...
Now if you add sounds, etc..., does everything work properly?
I no longer see corruption in Companion if I do this, but I haven't tried the game out to see if it can handle having 65535.map embedded in the main resource package instead of being a patch file.