My solution was to carefully verify that all settings were a perfect match. I had assumed that since I had set some of the settings to be the same, that those settings would no longer be in the generated change script. This is not the case, however. If there are any database setting differences, it appears to include others that ARE the same with the wrong value.
The settings I had missed were on the 2nd and 3rd tabs of the Database Settings dialog (Operational and Miscellaneous).