Flagged Drives Create Access Privilege Issues

Upon trying to open up permissions between 2 accounts in Snow Leopard I caused the os to crash - restarting/turning off then on did nothing - the os would no longer load. I took it into Apple where they got the os back up and running with a slight twist. The secondary drive was flagged (a little lock icon appeared over the standard icon). Basically this rendered the drive unaccessible. I used:

chflags -R nouchg /Volumes/Macintosh\ HD\ 2

via in an administrative account. This fixed the problem of access for this particular drive but left a soon-to-be-found secondary problem. Every drive that I would mount ended up mounting in this flagged state. I would execute the command above and things would seem to be fine. The problem occurs if and when I copy files from an external drive to the secondary drive. If I try to open those files from the secondary, the application responsible for accessing the files cannot access the files and throws an access privilege error. My main reason for copying files from external drives to the secondary is to take advantage of internal bus speeds for apps that use a lot of realtime processing.