Cannot access files after OS reinstall

I have a Storage Server 2003 with a RAID 5 array and two partitions (OS and data). I needed to reinstall the OS due to problems I was having with Shadow Copy (Shadow Copy Fails on Storage Server 2003). After the OS reinstall, there are some files giving me this error when I try to open or copy them: "Error 0x80070780: The file cannot be accessed by the system". I get this error locally on the server and remotely as well. However, other files will open just fine. I assumed that this is a permissions error. So, I once again took ownership of the network share. I deleted all the current permissions and reinstated them to no avail. What am I missing?

Cross-posted from http://social.technet.microsoft.com/Forums/en-US/winserverGP/thread/a0b2bb5d-4813-496c-a606-723324aaacd2 after I discovered that it appears to be all the files that were consolidated by Single Instance Storage.