Desktop acting like Disk Image?

I am having some very strange issues with my Mac right now. Whenever I try to move something from the desktop to the trash can, I get a warning saying the item will be permenantly deleted immediately. This is before I empty the trash. I am also having some issues when I try to update Adium or 1Password or a couple other programs I get a weird error:
Update Error!
1Password does not have permission to write to the application's directory! Are you running off a disk image? If not, ask your system administrator for help.
I know I have Admin rights, I have repaired disk permissions, I don't really know what to do next. I get some weird things when I do the Repair Permissions though. It says:
ACL found but not expected "Applications/Utilities"
ACL found but not expected "Applications"
ACL found but not expected "Library"
Thanks for your help.

Just an update on what I have done:
Did an archive and install at the recommendation of apple support and that didn't fix it.
After that they recommended I delete the user and then restore all the settings and everything from the disk image that is created. This actually fixed the problem, but now it turns out that the permissions on all the files are screwed up. Here is a picture of what it looks like.
http://skitch.com/adamteece/ghfc/permissions-issues
We tried to fix them, and I fixed a lot of the permissions but you have to go through file by file to change it. We tried resetting permissions from the leopard disk, repair permissions from disk utility, but nothing seemed to work. It is usable for now, but there are still issues here and there. I hope Apple will fix it. I am not the only one having this permissions problem now, here is a thread describing it better.
http://discussions.apple.com/thread.jspa?messageID=6699818

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