I have no idea what could be causing that problem, but I have some suggestions as to where to start for a workaround:
Try creating a new user account and logging into that. Then start up your applications and see if the same issue happens. If not, then copy your documents over into the new user account and use that account instead of your old one.
If the problem isn't localised to your user account, try booting Ubuntu off a livecd or USB stick. See if the problem still happens. Most likely it won't. If that's the case then one sure fire way to fix the problem is the reinstall Ubuntu.
I'd use the 13.04 live disc though, as there's not much point reinstalling an old OS version, unless there's a particular issue with the new version that you need to avoid.