Everything you have said points to one thing to me, a failure to
upgrade from 10.04 correctly. Correcting this has only one fix that's
worth the effort IMHO - erase Ubuntu and start again.

You say you have separate HD's for Ubuntu and Windows so the way to go
would be to disconnect the Windows drive then install Ubuntu 12.04 and
let it take over the entire drive. After that you can plug the Windows
drive back in and boot into the Ubuntu drive to automatically enable
dual-boot.

Once you have 12.04 installed and updated etc you won't have to think
about upgrading the OS for a full 5 years