Andy McNish
Don't install 3rd party VSTs under C:/Program Files or its subfolders. Quite often X3 won't see them.
Install them somewhere like C:/Cakewalk Content/VSTs and it's all good.

I have all my VST2 plug-ins installed in C:\Program Files\Cakewalk\Vstplugins. Also VST3 install in C:\Program Files\Common Files\VST3. I have yet to have a problem with X3 seeing any plug-in. Must be luck.

If you can scrape up the money, ($200, on sale these days) get an SSD for your c drive.  It's a whole different enchilada, from a load time/performance perspective.  Agree to letting X3 put it's stuff on the SSD/c drive...Then you can have your large drive for sample packages (you'll find you'll need it!) and the third drive for Songs...
 
Also, buy an inexpensive external 1/2/3TB usb2 drive for backups...$100 well spent.