I apologize if this has already been explained but it's a long thread and there seems to be alot of 'permissions' confusion here.
These files basically are the update. 'Repair Permissions' compares the permissions state of the system files currently on your mac to the 'install receipts' of the files from your original Leopard Disk. That's why the 'ARDAgent' file has been popping up for a while now. It refers to the 'Apple Remote Desktop Agent' that was one of the first Leopard Software Updates, which is why the file no longer "matches" the one from your install disk.
At some point the verbosity of PRepair changed to include these types of changes and they are not anything to worry about - which is why they aren't fixed. I think Apple mostly considers PRepair to be a more tech-savvy app when put in verbose mode ('show details') and that's why the messages can seem a little opaque if you don't understand exactly how the process works.
After the update these system files changed and no longer necessarily match the ones from 10.5.0, so you see this message in detail mode.
I actually noticed this after the update and thought, 'oh neat, there's the new stuff'. Some of it anyway
So, fear not.
Based on what you said, I have a problem with why the behavior is different if the 39 MB update is applied vs. the 110 MB update.
Also, it makes no sense to compare to the original install disk for anything that was updated...the receipts for the updates should be checked -- not the originals from the DVD.
So it sure seems like either the files were not actually updated...or the receipts were not updated...or per your explanation, Apple is stupidly comparing against the DVD and not the receipts from the update.
In the end, however, the behavior from the 39 MB update and the 110 MB update should yield the same results. Somethings not right about that discrepancy.
