Vista - pc decided to hide files

Hi,

Yesterday my pc took on a life of its own, the majority of desktop stuff
vanished and all files appeared empty. When I looked at the disk space it was
obvious they they must still be there as there was no more free space than
normal. I have manged to get vista to show me the hidden files but some are
still in a translusent type rather than normal solid colour. I have run
defender, anti-virus, anti spyware and even defraged , I have done a system
restore, with no luck. I don't know if this is also related but at the same
time I had trouble accessing task manager (now working fine) and another
program is not working that was fine before. I could quite easily go through
the folders and un tick the 'hidden' box box but I would like to know why
this has happened and maybe how to prevent further problems.
Any help greatly received, thanks.