I have only ever used ATI cards and I have NEVER EVER had this problem. I'm serious! I've had ATI cards going back to the AIW 8MB PCI card and have upgraded with at least a dozen and a half cards since then. This goes way back to Windows 95, 98, 98SE, XP Home Edition, XP Pro, and now Vista 32-bit Home Premium.
I've also used both Omegadrivers and NGO ATI drivers during this time. Mostly, though, especially since upgrading to Vista, I've stuck with the official releases of the drivers.
Another thing I can tell you is that I AVOID Driver Cleaner like a plague! That utility is a ticking bomb and needs to be discontinued. (Even the Catalyst programmers have stated as much in private but are afraid to make a big issue of it to avoid stirring up too much trouble over at another site most of us are quite familiar with.

) One of the driver developers did, however, state very clearly that the DC can cause more problems than it cures.
My own method of updating drivers is just what ATI recommends: Simply run the new version installer and let it do its job. Period. No uninstalling previous versions, no using the ATI Uninstaller, just run the new version installer and be done with it. That's it.
There are only TWO instances where someone needs to do a complete uninstall of the drivers in order to avoid problems...and one of these is optional if the following method is used:
1. Someone needs to uninstall a current version IF they are reverting to a prior version of the drivers. Either that, OR just be ready to answer YES at every prompt to OVERWRITE the current file. That's it! Nothing magical or conspiratorial is involved.
Those who use Omegadrivers and READ the instructions will be well-aware of the fact that even he advises to just run the installer and answer YES to any prompt to Overwrite newer versions of the files.
2. The second instance is IF the user is switching from Manufacturer Made video cards (NV > ATI or ATI > NV) In this case, however, it's usually HIGHLY advisable to do a complete OS Installation to make certain to avoid driver conflicts.
My personal advice, delete that Driver Cleaner program from your PC and forget you ever had it.
I've been doing this for YEARS on EVERY ATI card I've owned and very, very, very rarely is there ever a problem. In fact, the only times I can remember having problems is when I've tried to use an Uninstaller first.