Running out of ideas...
Does the original Apple remote show the same problem?
Another idea is to try changing the ID of your Apple Remote, which is done by holding down the Menu and Center buttons together for several seconds.
http://support.apple.com/kb/HT3176
Assuming those commands work, you could then try learning them on the Harmony. This is a long shot, since I think the things you've already done should have worked.
Does the "Unpair" command in the Harmony library work from your Harmony remote, or do you have to choose "Unpair" from the on-screen menu?