The one thing I will never have my repair program do (And why it will never be perfect) is change registry settings. Its like playing with fire. One wrong setting and a persons system is down.
So when a infection messes up the reg settings the best and safest thing to do is a reinstall.
First you can try a repair reinstall. If that doesn't fix it you will need to do a normal reinstall.
So far your problems don't seem to be permissions related. It looks more like reg keys where changed or removed.
While I may add a few reg settings (Only safe ones) down the road. The best thing you can do at this point is a reinstall
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Do you need any info on how to do a repair install?
Shane