This is probably because the affected applications (e.g. Skype) start on startup, but are up before unity. See https://bugs.launchpad.net/ubuntu/+source/unity/+bug/765269 comments 3 and 5.
-- You received this bug notification because you are a member of Ubuntu Bugs, which is subscribed to Ubuntu. https://bugs.launchpad.net/bugs/755234 Title: systray appears behind main panel/one pixel for some qt applications -- ubuntu-bugs mailing list ubuntu-bugs@lists.ubuntu.com https://lists.ubuntu.com/mailman/listinfo/ubuntu-bugs
