Lateral thinking
The assumption was that if TrueCrypt was compromised, then it would be somewhere in the encryption algorithm, but we don't give the intelligence agencies enough credit. Who needs a backdoor to the encryption if you have compromised the system, to among other things, obtain the password via a key logger?
No I'm not suggesting that this was deliberate, although I'm absolutely ready to believe that TrueCrypt has been compromised in some form. This does however remind us that there is more than one way to crack a nut, and that spooks would prefer a less obvious yet incredibly simple approach of pick-pocketing the key while their targets are focused on improving the lock.