We are seeing an issue where the portlet preferences are not being set (persisted in database either) when having a portlet embedded in the theme. This was working prior to hotfix-10946. I have attached a testing theme to demonstrate the issue. We only see preferences in the database AFTER opening up the portlets configuration panel, but it is also incomplete.
Velocity code for embedding Web Content Display portlet:
STEPS TO REPRODUCE
1) Install hotfix-10946
2) Start server
3) Go to the default site.
4) Add a "Page"
5) Deploy and assign the test theme as the theme for the page via page look and feel
The setting in the velocity preferences object are stored in database. Should show something like:
At first there was no entry in portletpreferences, then after opening the portlet's configuration in the page, the entry was added to the database but the value was <portlet-preferences />.