Well just a week ago i faced a very uncommon problem with my system,am using xp 2 as a substitution os with windows 7 using dual boot.But that day i found that all hidden folders in my computer got permanently hidden and when i tried to change the settings by marking the “”show hidden files”” at folder options menu it again gone back to, keep them hidden.But registry editing is the best option to treat any virus because everything is the magic of dwords.So here is the solution i got for my problem:
1.Open run window and type REGEDIT.(i.e. registory editor)

2. Go to the following path

HKEY_CURRENT_USER > SOFTWARE > Microsoft > Windows > CurrentVersion > Explorer > Advanced
On the right side, double click the hidden value and give it a value of 1.

3.Do the same for HKEY_LOCAL_MACHINE > SOFTWARE > Microsoft >Windows > CurrentVersion  >Explorer > AdvancedFolder Hidden>SHOW ALL
Change the  Checked Value to 1.

And now everything is ok…..!!!!