Hi,
I know it's almost a year late, but I have found the same thing. I'm currently running 10 SP2 and I had also lost the ability to get any of the right-click menus to load.
I had even recreated my normal template from scratch, which seemed to work until I added all the toolbars again. Your thread prompted me to look at PerfQAAnalyzer. Sure enough, once I had removed the toolbar and restarted ArcMap, my right click worked again!
This isn't really a solution, but hopefully it has been fixed in the later service packs?