I have a similar prob. The VST scan in X1, 2, & 3 is showing duplicates of every instrument. Although this doesn't affect Sonar's functionality, it shouldn't be happening.
Deleting Registry Entries CAN be sometimes scary. I found 10,000 entries for one VST that needed to be deleted. For that you need a utility willing to find and delete them for you, unless you have several years to delete them one by one yourself.