Apologize for missing this post. Were you able to resolve the issue?
The template did not save the favorites, that option was not set...
An easy way to add them would be to open Firefox with Application
Profiler, start your modifications (add favorites for example), then save the changes with predefined settings.
Also, you can, within App Profiler, you can choose to uncheck "Enable Registry Exclusions" and uncheck "Unable File Exclusions". This will give you more granularity but also more informaiton to parse before saving.
I have the same issue as outlined above. I did modify it and saved a favorite. Changed the home page. Added a few exceptions. Works fine from the same server - but the second I try from a 2nd server no data is retained. This however works just fine for all other apps including IE.