I ran into a similar problem w/ an AT&T branded w580. I got flash menus to work by creating a customize_upgrade.xml with the following:

<?xml version="1.0" encoding="UTF-8" ?>
<customization>
<flash-desktop>
<settings reg-path="/apps/flash-desktop">
<enabled>true</enabled>
</settings>
</flash-desktop>
<mmi>
<settings>
<enable-flash-desktop>true</enable-flash-desktop>
</settings>
</mmi>
</customization>

Make sure the customize_upgrade.xml is in the same folder as the customize.xml (tpa/preset/custom/). Also I didn't have to do a master reset or anything after turning the phone on, but I would back up everything just in case!