Hello Nelsson.
- resolution problem existed in 9.04 too and was solved by adding following 
line to xorg.conf: HorizSync 30.0-100.0
I think your monitor was not recognized by Xorg. What model do you have? Attach 
Xorg.0.log file with option "HorizSync 30.0-100.0" and without it.

- missing graphics in several programs
Attach the photo/screenshot of the application that have missing graphics.

- square mouse cursor was present when upgraded to 9.04, but was fixed by a 
patch (don't know which one though). 
Please check which patch fixed your problems with square mouse cursor.

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[K8M890]Square cursor with Ubuntu 9.04 livecd, during VNC connection
https://bugs.launchpad.net/bugs/377402
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