This has gone on for such a long time now and Steinberg said it was fixed, every launched causes media bay to re-scan the VST3 folder with all its presets and has to re-populate it.
My Documents are located to another hard drive so all that stuff is off my SSD (using windows to relocate the data).
The user VST3 folder is in Documents folder on this drive.
Why on earth is it doing this?!