Examine your Logs for errors.
Anything that gives you an error, either update it through SVN, or archive it and delete the original folder, until some time has passed and relevant updates have been pushed through SVN.
I had the following stuff that gave me headaches.
-Combat routines other than Singular.
-AutoEquip needed a refresh of its Weight Sets, since I use custom ones, which I had to manually install again in place of the defaults. Shouldn't be a problem for people who don't mess with the Weight Sets.
-Bots such as BGBot and ProfessionBuddy refused to fully compile, causing Honorbuddy to freeze when I hit START, so they had to be archived and their folders deleted to prevent HB from trying to compile them.