I've got a 2006 core duo intel iMac 1.83 Ghz, 2 gigs RAM running Snow Leopard. I tried the cleanup function on a free program from MacKeeper.com. It froze up twice in the same place so I just deleted the program but I think it shuffled some things around.
The Computer seems to have all my files but the startup window with accounts came on without my picture [?]
Running Disk utility permissions is also strange. In verify permissions after the list of permissions to be repaired It shows the following:

> Warning: SUID file "System/Library/CoreServices/RemoteManager/ARDAgent.app/Contents/MacOS/ARDAgent" has been modified and will not be repaired."

The repair function goes through with radically off time estimates to the order of 57 minutes but instead finishing in 5. After permissions repair complete, when reopened, disk utility 'verify permissions' finds another fairly long list of items with altered permissions and the same warning at the end. Previously running this utility would repair permissions pretty much completely until there was a new software download or update.

How do find and fix this?

Hi, and welcome to FineTunedMac.

I can't help you with your issues, but I just took a look at a bunch of the comments posted on MacKeeper's MacUpdate page, and I wish you luck.

Read Mac OS X: Disk Utility's Repair Disk Permissions messages that you can safely ignore. I also get that wildly inaccurate estimate of time to repair permissions, and I haven't used MacKeeper. This has been "normal" since 10.5.

I've gotten consistently short estimates, a minute or two, that match Disk Utility's run-time since I've been running Snow Leopard; I believe Leopard also gave me short estimates and runs (although not as short as SL). I skipped Tiger and can't speak for it, but I remember Panther as the OS that took gave me absurd estimates and took absurdly long to run.

My recollection is a bit different. I remember Panther and Tiger requiring only a short time to repair permissions. Leopard, IIRC, had the problem of taking 20 minutes or more to repair perms. This was fixed in Snow Leopard. For me, repairing perms in SL takes only a few minutes but the estimated time is way off.

Your memory's on the mark, Jon (but, after all, you do repair perms more often than most of us ).

I just booted into Leopard... 20 minutes of "Reading permissions database," with no attendant time estimate other than "Reading the permissions database can take a few minutes," followed by a 1 hour 20 minute estimate to complete that worked itself down to 5 minutes in about 30 seconds and completed in 3 minutes.

Aaargh!!! No wonder I forgot about it!

Thanks all especially the post about what can be ignored in verify permissions. Tiger was as predictable as sunrise with this utility. Estimates were linear and proportional. Permissions stayed repaired. Not so at this point with SL. Though the MAC is running smoother now that it has been run a few times and MACkeeper is gone.

Glad to hear things are looking better.

If you haven't done so already, I suggest that you shut down your Mac and then restart it; it sometimes does stuff we can't begin to predict.