I have use Smart Start multiple times to include devices with the security turned off, works great. Just be sure the device is powered off while you set it up in SS, then turn the device on. Also, not sure if its possible, but did you by chance have the device added to SS multiple times with different settings?
This driver works with S2, and was originally created by the dev who eventually created the app. [BETA] Updated binary firmware updater
Also, you can use a secondary USB zwave controller to do the firmware updates.