> I upgraded my system, including the version of Firefox.
> [...]
> Sorry this is a bit rambling, but its very hard to describe!

A picture can say more than thousand words.
Can you reproduce this with a simple configuration?
If yes, can you attach the configuration, the *a.log files,
a description of what firefox version you're using and please:
some screenshots of "before" and "after"?

Thanks!
Andreas