There's two primary functions of a hard drive: read and write. Reading is accessing information, writing is being able to access/move it.
Now, when you boot up a PC the heaviest portion being used is the read function, which is the most common to go out on hard drive failures. Which in this case would explain the chkdsk and inability to see your folders; more than likely the read function is dying out, causing the OS to try and auto-repair "its" issues and having subsequent partition damage - why your files still take up space but you can't access them.
This is going to come down to how severe the read portion of that drive is gone. I would try an external closure to see if hooking it up outside of any connection to the other HDD/OS renders any success. If not, then maybe an application would help, but I'd doubt it (and as you're seeing) because you're battling hardware and potential OS corruption, not just OS corruption which is what a lot of those applications are more geared towards in term of recovery.
Now if you get really desperate there's always the trick of dropping the hard drive from about 2-3 inches to attempt to release the headers. But I'd only try that if you were using an external bay and it was the last ditch attempt.
Last edited by Vilgent; 01-27-2009 at 11:27 AM.