I ran disc utlity and it came across a lot of errors. But the one thing in common with all of them is that they all start with "ACL found but not expected on" and then it shows a bunch of applications.
Actually, just do a software update. ACL's are normal, but when Leopard first came out, Disk Utility didn't know that and would report them as problems. In 10.5.1 or 10.5.2, that problem was fixed.