A guildmate had a problem recently with TTC installing in an unusual way, so that they ended up with a subfolder within the usual ESO folder with a copy of all the game files, and launching the game from the subfolder rather than the original install - and the result of that sounded very much like you describe, with addon settings not being remembered between character loads.
Have a look at the folder structure and see whether something similar is going on for you.
Sorry I cannot be of more help as I didn't experience the issue myself.