Im using SATA drives throughout.. no numbers.

Actually - I was wondering about this.

Im using 9.04 now. I moved from 8.04. When I installed 9.04 I linked to
my original /home drive. I have noticed some little problems like - on
Terminal - its not transparent like on my default 9.04 install - its
transparent all the way through to the desktop instead of the window
beneath. Little things like that. But I was wondering if perhaps I
brought over something else, dont know what as this is really outside
anything I know anything about, but some file setting or drive setting
in /home that is causing this problem.