In reply to sserraph:
I was having the same problem with 3.4.1. Try the 126.96.36.199 update. It seems to have fixed the issues I was having with 3.4.1. I haven't completed an unlocking quest yet, but the quests I have completed are automatically being recognized. Also, all the broken recipes in 3.4.1 appear to be fixed as well. I'll post again once I unlock a new stage.