Internal HD has a problem?

Ok here is the situation, I was haveing some issues with me internal HD with Snow lepard. Finder was acting funny freezing up and getting snotty. I tried several thing like Disk repair verify permission all that. MY disk drive I believe isn't working properly because I never use it. So I could use the OS disk to start it. HD issue was a directory error something about the an incorrect item count of 31 when there should be 32. YOu guys might now about what they is. In any case, Lion came out so I decide to just download that, now don't get nervous I downloaded it to a completely sifferent HD and the MAc is running fine from that and everything is really cool. Now my issue is that the HD that had snow leopard on it for whatever reason I can't partition it or reformat it with Disk uttility. I can access it through lion like a normal Hard drive and go into the files and such but I don't need it and would like to reformat it. So the long and skinny of it is, is the HD junk or is there something to get over this issue. The HD is 320gb so I would like to be able salvage it to reuse but if not no biggy. Is there a different way to get at that drive so I can getting working.

The position of the HD icons on the desktop is (irritatingly) no longer relevant. I'm not sure when this changed, probably an update or two back.
To verify the startup disk in use, go to System Preferences>Startup Disk: the disk in use is highlighted.

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