The problem is, there is no "CTRL-," or "CTRL-." codes. Hex codes 2c and 2e are plain old comma and period. There's no way for ne to know that you had the control key pressed when you hit the comma or period keys.
If you fire up ne and invoke the "KeyCode" command (^k then "KeyCode" or "kc" and hit enter), you'll be prompted thus:
Press a key to see ne's corresponding key code:
If you then hit Ctrl-, for instance, you'll see:
Key Code: 0x2c, Input Class: ALPHA, Assigned Command: (none)
Key codes with "Input class: ALPHA" cannot be reassigned. If you somehow
did reassign those codes, you would no longer have comma or period keys.
On my machine, Alt-, and Alt-. (1ac and 1ae, respectively) are both "Input Class: COMMAND" (i.e. you can assign them in your .key file) and "Assigned Command: (none)" (i.e. they aren't currently mapped to anything).
Hope that helps.