Aha. Maybe Logix is trying to take the old activation. Whether that's because the new activation is being "held onto" by some other instance of the software that didn't shut down properly (or something), or because Logix just has it's knickers in a twist and is playing dumb, I guess we don't know.
I do remember that when I put my new activation on last year, it took me a while to work out how to get rid of the old one. It wasn't causing me any problems, I just have OCD
Unfortunately, that was nearly a year ago, and I've forgotten. Which reminds me, I need to follow up this year's renewal...
If rehosting is not an option, perhaps try browsing to the folder where the .lic files reside, and deleting the old one (obviously, double check which one is which first!). Then refresh your server, refresh your activations, restart Activation Manager, restart your PC, stand on one foot, spin around counterclockwise twice and pray to the gods of Rockwell Activations, and see if that helps your situation at all.