After copying over my characters, I happened to look at the adventure compendium and noticed my total favor was wrong. Tracking down the missing amounts, I noticed the following quests are missing from the compendium (thus granting 0 favor for completion):

A Cabal for One
Prison of the Planes
Madstone Crater
Gianthold Tor
The Reaver's Fate

I logged out/in to try and correct it, and jumped onto other characters to confirm that it is not just 1 character that is screwed up: it's not.

Bug reported as well.