I found this thread after having the same problem with my new car, a 2016 Volkswagen Bus supporting AA also and containing two USB ports for misc. connections (including AA).
I have an even worse effect: If you use the USB port without AA (AA even not installed), my phones (OnePlus One and a Nexus 5, both with Android 6.0.1) show the charging battery icon. If I installed and activate AA on the phones, the charging icon on the phone is shown for approx. 3 seconds after connecting the phone to the car's USB, then it dissapears again. Means I see that the phone itself disables charging after switching on the AA mode.
Before reading all your posts, I thought the AA app itself prevents charging - for what reason ever. Now I think it's just the (low) amount of current flowing into the device that turns the OS to stop indicating charging.
This leads to the assumption, that even if AA is deactivated, the indicted charging of the phone is negligible in the VW Bus, possibly a similar weak power supply in the USB ports like for the Pandora... :-( Have not yet verified this sufficiently, but will keep you updated...
Hell, I've spend a lot of money to get USB ports in the car, mostly for being able to charge the phone while driving, and not using the 12V power supplies in the cigarette lighter...