I don't think this is a common problem, but unanswered questions found in my failed Windows 7 searches suggest it's not rare.
I ran into the problem after my corporate laptop died. This happens fairly frequently, I suspect the encryption software we use great increases the risk of unrecoverable errors resulting in effective drive failure.
Since I was traveling I knew I'd lost a bit of work, but fortunately my notes were still on paper and I run my own automated office backups  using Retrospect Professional (Retrospect Windows now). I was a bit nervous though, because I consider backup to be an unsolved problem. Even though I do a test restore to my system every few weeks I still don't trust my backups.
Despite my worries the restore went well. In an hour or two I had 30 GB of Windows 7 data I could access from a workstation while I waited for my laptop repair.
Except ... I couldn't see my User Folder (ex: User/jgordon). I could see other folders, but not my User Folder (where most of my data was).
I knew my files were there, something was taking up 30GB of storage. Retrospect could see the files, Windows 7 couldn't. (Later I showed that XP could see them too.)
Hilarity ensued. I'll spare you the details of the fixes we tried including icalcs resets, updating access privileges for all children of the visible container folder, escalated privilege command.com and so on.
The trick was a setting in "Folder Options" that's been around for over a decade, but whose meaning changed @ Windows 7 (Vista). In Folder Options find and and uncheck the "hide protected operating system files" option. Suddenly everything appeared.
Why was this so hard for us to figure out? There were several contributing factors:
- Google was no help. Even after I knew the the cause of our problem I couldn't find an answer on the net (now there is one).
- This didn't come up in my test restores because I was restoring to the same User Account I backed up from.
- This is an old setting whose meaning had changed. In XP, even with this checked, I could see all User Folders.
- The setting impacts all access, not just Folder Access. So it's in the wrong UI location. The folder was invisible to the command line utilities too.
- This setting is orthogonal and independent of all user and permission settings.
- On my own systems I routinely make everything visible, so I'd forgotten that wasn't the default on the workstation I was temporarily using.
Like I said, backup is an unsolved problem. 
- How do I restore security settings to a known working state? (Win 7 equivalent of OS X Permissions Repair)
 There's no officially supported way to backup a large personal drive where I work. This is more common in large corporations than civilians could imagine; I have far more robust backup at home than at work.
 To solve it vendors would need to design the OS to facilitate backup and restores. Apple did this to some extent with iOS.