I ran into this after reinstalling Skyrim a little while ago. All of my trainers added by mods stopped working. You could ask them for training, but then nothing would happen. The training window would just never come up.
I did some experimenting, and found that after deleting the training dialogue, and creating a new one, they worked again. Even though I created the new dialogue exactly the same as the old ones.
So if anyone runs across this bug, that appears to be the fix.
While we're here, I'm trying to make Dawnguard work in the CK. If I toggle Dawnguard.esm and try to work on it, the CK just crashes though. I know for Oblivion we could toggle bUseMultipleMasters to 1 but I don't see this line in Skyrim's confi file.