At the moment I'm trying to remote control my machine and command and ctrl do not seem to be working properly. Is there some type of 'keyboard sniffer' functionality so I can see exactly what is and is not being received?
I don't know if the built-in keyboard viewer is sophisticated enough, but it should highlight pressed keys.
If you do not see those options, make sure it is checked off under your System Preferences > Keyboard
There are also apps like Keycastr that display bezel elements for pressed keys.
The application Key Codes from Many Tricks, available for free from the App Store, displays the key code, unicode value, and modifier keys state for any key combination pressed on your computer. If you need more extensive information than that provided by the Keyboard Viewer, you might find it helpful.