Some more information on the problem. I went into the Stardock download folder and manually ran the Fences 4 beta installer and same problem. I also noticed that Fences and Fences 4 beta were listed as separate programs in ODNT, but only 4 Beta showed up in Add/Remove. I then uninstalled, rebooted and neither version showed up in ODNT or Add/Remove. Then I installed Fences 4 beta, again through ODNT and it once again immediately said I needed to update from 3.98 to 3.98.54. Even though that's what I had just installed.
I cannot at this point tell if the issue is in the installer directly, or maybe the data it is writing somewhere that ODNT is reading it?
The only other anomaly I noticed is that in Add/Remove it is listed as Fences 3.98, not 3.98.54.