There is a bug in Mac OS Panther 10.3.x and iTunes 6.0x that will prevent Disk Utility from repairing permissions. When you try to repair permissions, it will stop with a "Lost Connection" error. To fix this problem, simply remove the iTunes reciepts from the /Library/Receipts folder. Once removed, you should be able to perform repair permissions withtout any problems. Hope this helps, it took me several hours to figure out.
[
robg adds: I did a bit of search work to try to confirm this one, and found
this thread on the MacFixIt forums. In there, it states that what you want to remove are any
older (pre-6.0.2) iTunes receipts folders. I have not tested this one myself.]