RegScrubXP is almost always safer than RegSeeker, imo. I have never ever used RegScrubXP where problems occured afterwards but on some certain -already- troubled systems, RegSeekers quite agressive cleaning did a bit of damage, nothing huge but still noticeable and annoying nevertheless.

That is why I generally use RegCrubXP and recommend it but further more, whichever one I use I always run ERUNT first, then run one or both of them then reboot afterwards BEFORE INSTALLING or doing ANYTHING else!
That way if a problem surfaces you will have a better idea of what caused it and how to go about fixing it, etc.

If you ran both and opt'ed to have them clean whatever they found, at this point the previous one at-a-time registry troubleshooting is the only thing I can recommend.

Here is another silly sounding idea that might help us understand more of this problem: download and use a free alternative program such as my personal favorite: MyUninstaller.
See if it has any issue displaying the entire list?