Preliminary Implimentation:

now I by no means claim to of completely beaten this problem, but I've come up with a neat and simple way to identify whether players are using 'non-standard' code.

I've put the full description here but basically it boils down to this:
a private message is stored in both the server and client, to check the client isn't using modified code, the server sends a request to authorise followed by some random numbers. the client performs a one way hash using a combination of these numbers and the (constant) private message and sends this back to the server. Said server then checks that the correct private message was used to generate the hash, if it wasn't, then the client is using modified code (since it was built using an incorrect private key).
this also bypasses any requirement for file checking and other nasty system dependant checks, and keeps everything nice and clean.
Another benifit of it is, you can also prevent old client builds connecting to new servers, whilst still allowing new clients to connect to old ones.

Client code is included in the 1.7 engine source -including the SHA1 code used in the server

Server code: Will be added to the project when I have the time (or if you want just request it)