mmmatt - I've had the EXACT same problems as you. I had 2 hard drives in my machine, one with my program files (C:) and another huge drive that I was using just for storage (D:) - I did a reformat of C:, and all of the sudden, many of my flac files would not decode - both on D: and on CDs and DVDs I burned. I've given up on trying to fix them, and have sworn off flac becuase of it.
I think my issue was a drive corruption - after the reformat, I made a new directory on D: that was all of the .wavs from old flacs that I could actually decode, and they were all being saved. The resultant .wavs coud be played in several audio programs. I got Nero, and tried to burn the .wavs onto a DVD, and the directory was corrupt. When I clicked on the directory, it gave me a message that the directory was incomplete or corrupt - and this was not flacss, but wavs. I don't know if my reformat of c: caused the corruption on d: - unlikely b/c they are physcally different drives.... or if it was just coincidence....
I've had several discussions with freelunch and a couple w/ MikeW, and done hella searches online, and nothing has worked. I searched the exact error text online, and most resolutions were achieved through re-downloading the original flac files, indicating a partial copy of the flac. I've since started using a prog called "copy large files" to move the wavs around, per advice from Freelunch about losing data when copying - he uses rsync, but I suck at command line stuff, so I needed something with a nice interface.
It really sucks, but I'd bet money that your drive is dying. Exactly the same issues I had. Unfortunately, I'm not sure if you'll be able to recover your FLACs. As much as I liked flac, I'm done with it. At least with some other file format, the audio would be somewhat salvagable.
sorry bout your luck dude.... I was there... I'm still there.... just had to come to grips with losing all kinds of stuff I considered rather valuable. 'twas my first hd failure.