Permissions not repairing

Hi,
Setting up my wife's new mac mini today. used setup assistant to transfer users and settings from my mbp running 10.4.11 which was updated and permissions repaired before doing anything. i did transfer everything, applications, users, files, etc. (maybe i shouldn't have done the apps) anyway, things seemed to go smoothly.
then...
repaired permissions on mini before taking software updates--ok
took software updates, restarted--ok
repaired permissions again and there was a ton to fix.
did followup repair to see if all were caught. but they weren't.
repaired again. but now keep getting the same results over and over.
three are related to system/library/frameworks/java...
comes back saying those three are repaired.
also get five "Warning SUID file ....... has been modified and will not be repaired.
after repeated attempts i keep getting the same results, whether i do restarts in between or not. i figure sooner or later these bad permissions will come back to bite me if i don't get it fixed. suggestions? should i start over, erase and install but this time without the apps.

BB623 wrote:
What causes these to be issues in the first place?
The short answer is the cause is differences in the permissions database the process compares to the item's actual metadata. Permissions can be "repaired" only in the sense that they can be reset to what is in the database when the two differ.
So for instance, if an OS or application update doesn't update the database as well as the item itself, you get a message telling you about that. It isn't an error in the item, just in the database, & the process is smart enough not to "fix" the item … which actually would be an error!

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