Bodgeit: Don't be so sure about Thief 3 GOG version,I have it installed & found this in my registry the other day while I was doing a clean up of old entries from other games.
Was going to contact support once I finish the game if I can't delete it from the registry without the SecuROM removal tool.
AB2012: Those are just passive text error messages that can be (but aren't) called by the DRM that's no longer there. The disc version originally had SecuROM 5, however if you install the official editor the original SecuROM'd .exe gets overwritten with an v1.1 executable with no DRM. "Sneaky Upgrade" does the same thing. GOG has pre-patched their version in the same way. Game runs fine with Process Monitor (the thing that triggers FEAR) running. The only registry entries actually required by the game are:-
[HKEY_LOCAL_MACHINE\SOFTWARE\Wow6432Node\Ion Storm\Thief - Deadly Shadows]
"path"="C:\\Games\\Thief 3"
"ION_ROOT"="C:\\Games\\Thief 3"
"SaveGamePath"="C:\\Games\\Thief 3\\SAVES"
Everything else like the \SecuROM sub-keys are extraneous leftovers. If you zipped the game folder up, unzipped it on another PC and added above entries (correcting for location), it should work fine. In fact I don't even have the \SecuROM and \Locale keys on mine. Try backing those keys up and deleting \SecuROM and the game should run fine. It's just another example of how the registry is absolutely plagued with clutter.
Knowing that F.E.A.R. is now being entered into the GOG Preservation Program, did they actually do anything about those SecuROM remnants? Judging from the changelog alone, I would say no, but since I'm on Linux, I'm not the most typical user to verify this matter.