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If you start from runlevel 3 via startx, can't you switch off desktop effects and then go back to runlevel 5, reboot, and see if it works?
It sounds like the problem you are having does not directly have to do with your X installation (since you say you can use X from a manual start in runlevel 3) but more likely has something to do with KDE / Gnome or the GDM runlevel 5 login manager.
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