Permissions aren't fixed

I can run permissions over and over and DVD player and assorted Widgets always come up as being repaired. This is after I have thrown the Widgets in the Trash and even tossed their .plist files. I have reinstalled iLife 2006 to see if that would fix DVD, to no avail. I had to send a new iMac back with a fan problem, and that is how I noticed this problem. When I migrated stuff from this (eMac) to the new machine it brought all the problems with it. When I get the replacement iMac back I want to avoid the same situation. Can I just drag the applications and folders from the eMac to the iMac, or should I still use Migration Assistant? Here is the log from the last permission repair. The three before it are identical.