It appears that there are two places that addons can be configured, One in conf/services/addons.cfg, and one in userdata/etc/org.openhab.addons.cfg. The configuration file in userdata is where the dynamically added addons get written. I was having problems with addons getting uninstalled until I removed the conf/services/addons.cfg file and relied on the dynamically written one in userdata instead.
