Though I'm not completely sure, I wonder if keys that are mapped through the registry (mapped at the system level) might not be considered modifiers anymore... I'm not totally sure, but if you'd like:
Open Regedit
Navigate to HKEY_LOCAL_MACHINE\SYSTEM\CurrentControlSet\Control\Keyboard Layout
Within the Keyboard Layout folder (don't go any lower), see if you have a key called "Scancode Map". If not, create a Binary key called "Scancode Map", and edit the binary to read:
00000000 00000000 02000000 00001DE0 00000000
Then restart your computer.
For understanding:
The first 16 zeros are meaningless for these purposes.
The "02" is the number of keys you want to map, +1.
The next 6 zeros... Also meaningless.
The next 4 zeros is the scancode you want to map TO (0000 = Nothing).
The next 4 Hex digits are the scancode of the key you want to change (1DE0 = Right Control).
Last 8 zeros... More filler.
Scancode Mapping
In case your worried about losing it as a script hotkey, you can map it to any scancode... And I'm sure AHK has the ability to act on scancodes as well as keys. I think they call them Virtual Keys in AHK. Just remember the scancode you set it to, and make sure the scancode isn't in use by something else (unless you wanna map 2 different keys to do the same script, then go hard).