For reference, GCHQ's puzzle is:
If Samuel transcribed what Louis wrote…
…and Louis wrote what Ludwik translated…
…and Ludwik translated what Tim said…
…then what did Tim say?
Here is Samuel’s transcription:
IN AAAAIAN INAAANAIA IA IAINA AI AA IAIIA IAA AAIAAINN AA IAAANN IAINANI
NA ANNNNMA NAANIANMN NN ANNAN NN AM MNNNN ANI MAAINNIA AM NNAMIA NNAANIN
AM MMIAAMA MMIMAAMMA MM AMAAA MA AM AAAMA AAA MAMAAAAM AM AAIMMM MMMMAMA
CLUE: The key to unlocking the puzzle is identifying Samuel, Louis and Ludwik. There are links between them!
Anyway, after about 15 minutes we had the answer (which in lowercase and without trailing punctuation should have a MD5 hash of 29fa3b97488c805267461800b3c5d1a3). Turns out that if you throw a half-dozen software engineers at a puzzle it gets solved fairly quickly!
Warning: spoilerish notes ahead!
Samuel's transcription was solved fairly quickly once we worked out who he was, and the act of doing so gave a hint for how to understand the rest of the names. As soon as someone mentioned Louis' full name I realised what he'd written and set about reversing it (as it happens I've stumbled across a geocaching puzzle or two that uses a similar trick). This revealed Ludwik's message which looked like not quite gibberish and we were stumped for a bit as to where to go next - we had a good guess for who Tim was, but Ludwik remained elusive and with that the solution. Someone happened to mention a possibility for Ludwik's translation, threw it at an online translation service, and got the answer out (or rather a partial answer - he'd missed a couple of letters in his conversions and the online service didn't understand one word, but it was good enough to find the true answer)!