I just hit something very similar in 1.4.1 see http://forums.obsidian.net/topic/89445-141-quest-catch-up-on-rewards-of-feats-hits-progression-break/

Still not fixed nor reset. Still can't play quest mode.

I have experienced a similar issue related to awarding Power Feats (it breaks if you ever have to assign two Feats after one Scenario). The workaround that I employed was to delete SLOT99 and play without the affected characters until (hopefully) the next patch. So now I have 7 level 40s and 5 level 38s who are waiting for Feats and a patch before they can be used again.