I know this posting is over 4 years old but it's applicable to my situation and I'd like the archives of the internet to hear my words for other people's reference.
My 2011 XU has been acting similarly. I bought it cheap recently because the PO said it had a dead battery and wouldn't take a charge. This was entirely true, but I don't think it was because the battery was bad. You'd turn the key on and all the 12 VDC stuff would work but the battery gauge would flash with two bars, the red hazard light would randomly flash (even with the kick stand up), and the BMS would randomly beep. Nothing consistent would happen out of the whole bike other than acting weird once you turn the key on and never move. Once I got it in my garage I ripped the battery pack apart, then for SnG's I laid the pack back in the bike with BMS hooked up but hanging off the side, hooked it up and by some miracle everything was systems go! Battery showed half life, no weird flashing or beeping, and a slight roll on the throttle would creep the bike forward. Except, after a few times cycling this the hazard light started flashing weird again. No extra beeps, just flashing weird with no sequence.
Long story short, that stock BMS and MBB are crap and makes sense why Zero wanted all the older bikes off the road. When I talked to the local Zero dealer here in SD and told him I have a 2011 XU he seemed shocked one was still on the road, and working none the less. Turns out Zero's buyback incentive was aimed at getting all their bad engineering off the streets. Well, mine's on the street and gutted from all that "bad engineering".