I have had that - suddenly all VST effects are VST Instruments etc.
But even had that in Sonar 8.
Guessing mixing Sonar 8, X3 scans share something about plugins.
And doing a cumulative scan in new Sonar did that too.
Complete reset of plugin list and rescan fixed it. Also had duplicates looking in registry one scan was followed by another, so they were duplicates actually. But at that time, I manually removed all those entries - and made rescan.
Nothing about adding removing scan paths and stuff though, but never changed it either as I recall.