So, it seems the game try first to create the doomkey file in the same directory as pak000.pk4 file. If it fails, because you don't have the necessary rights on this directory, the game create it in home. But then can not find it or read it.
Putting the pak000.pk4 file seems to force the game to add the ~/.doom3/base as path.
Sure, it's more secure to have it in home but what happens if you put the doomkey file where's pak000.pk4 file installed ?
Need help with one of the installers?