They are identical below the surface and they're always upgraded at the same time. Because USA Today controls the ads for MileTracker, there are some extra problems it has (such as the recent and obviously unintentional popup) that MilePort has never had. That popup is gone in the upgrade.

Marriott is working again but just for the balance. Status, recent activity, etc. are disabled. Make sure to switch your login to an email address or account number since Marriott has phased out usernames and MT/MP will report an invalid login if you leave your username in.

I'll bet (or rather, hope) that everyone reporting upgrade troubles is running Windows Vista. There are known problems with that OS that have not yet been addressed. For now, if you are prompted for an upgrade, just click no, close the app, download the latest full install from http://download.deskport.biz/MilePort.exe, and install it over your existing install. There's need to uninstall and you won't have to reenter your settings, though you should back them up occasionally anyway either under the File menu or by copying MileTracker.settings. It's a hassle but it works. The upgrade is nearly the size of the full install (5.7 MB vs. 8.5 MB) anyway.