2300 miles since the BMS replacement, no BMS problems. We haven't had much rain recently, but it's been out in some pretty heavy rain since.
Had some pretty heavy rain yesterday and today, saw a two-flash followed by three-flash error message on my ride back home. Manual says its a CAN error. No effect on bike operation. Cleared up after it dried at home.
I lost three of the fasteners to the top trim plate on a recent ride (pro-tip: don't fasten gear in the tank position and then ride on really rough roads). I moved one fastener up to secure the trim plate, but suspect water got into something through the two remaining holes. Lesson learned. Edit: heavier rain today, fasteners replaced. No problems.
I believe the BMS can be set to a ZF3, ZF6, ZF9 pack configuration. I wonder if perhaps yours is unconfigured for some reason. If you have access to a serial cable to talk to the BMS then you can probably fix the configuration.