Problem with plugins/effects missing

Hi folks, Apologies for the long post in advance.
I have a problem where most of my FCPX plugins have disappeared from the motion templates folder, along with there respective Compositions folder the Generators folder and the Tittles folder, the Effects folder and Transitions folder are still there but with just two plugins left in them most have gone from those folders as well.
What is strange is that if I open and close Motion, the folders reappear and I can then reinstall the missing effects in to them and they show up in FCPX, Great, but! when I restart the computer the same folders and plugins are missing again.

So I uninstalled FCPX, Motion and Compresor using the Digital Rebellion software and downloaded all three programs a fresh from the app store, but the same thing is happening.

alI was well until I installed some updates from the app store today, and its quite possible, FCPX was updated when it didn't need to be (it was already updated)

any suggestions/ideas very welcome:)

sounds like a bad hard drive to me

Thanks for your reply anickt. Its strange that none of my other programs or plugins are being effected though, just 3rd party FCPX plugins and three out of the five folders in the motion effects folder.

Permissions maybe?

It looks like at the moment I have been able to keep a few effects in there folders, and I can now see them in fcpx, I still can't see my footage in the main window, but its there in the event window and in the project storyline, any thoughts ?