Ability Drain found something to try for the bug after fighting Alexius. John Epler says there is a fix in the works, but I haven't seen him mention an ETA on it. This fix doesn't work for everyone but it's something you can try.

Also, Aimo has a note on a bug in the later part of the Therinfal Redoubt mission, when siding with the templars in "In Hushed Whispers". In the quest after that, many things are broken. I don't know if they are the same one - once I get some more info I'll post it here.