Yeah.. the only other thing I can really think of is a malfunctioning rear derailleur, unfortunately.
This can be tested by any bike shop using their SM-PCE1 / SM-PCE02. You would just have to bring the rear derailleur to them and ask them to run error checking on it.
(probably best give them a call first though)
Note: you may also be able to perform error checking using the new E-Tube App (v4.0.2) and just the charger.. I haven't tested that yet :}