I've looked for this problem but not found it, so sorry if I missed the solution.
I upgraded from 3.3.2 to 3.4 and all my plugins vanished. There was a long list of messages saying they were deactivated because they did not appear to have a valid header. The files are still there. I tried reinstalling some basic ones (akismet) but they won't show on the list. I tried switching to the default theme in case it was a theme conflict, but no difference.
I know now I should have deactivated my plugins before upgrading, but I can't do that now since I can't even see them.
The site is here: http://evamoon.net/blog
If you can help or point me to a solution, I'd be very grateful!