Are you using a custom plug-in layout menu? If so have you checked the "Default All Plug-ins" menu to see if it is in sync with what you actually have installed?
Was there a point where everything was working? and if so what changed? For example did this happen after upgrading to X1d?
Also, as a rule I avoid using any system folder as a container for my plug-in folder - i.e. I never have my plug-in folder within 'Program Files', 'Program Files(86)', etc..These folders are protected and some plug-ins won't work properly when placed within.
While some may argue that they don't have problems having their VST folder located within Program Files - I've never had to modify or disable UAC behavior on my PCs to fix a DAW or plug-in problem.
*** EDIT ***
If you got this reply as a solid blob of text my apologies.
I reopen this message in Chrome to fix the formatting problems this board has with FireFox.
This forum has had a compatibility problem with FireFox since it last major update. I've filed several bug reports but the problem still exists.