Mine did the same thing. There were some updates that for what ever reason did not automatically download to my trucks system. Took it in to the dealer and the service tech manually downloaded the updates and after that the stop/start would work as soon as I let off the brake. So I don't know...
Is there a gauge either programmable and have show up in the instrument panel or an aftermarket gauge that will show the voltage and or the percent of charge the battery has?