Had the OS update issue when I was trying sending sysex with the Midisport2x2. Strangely, doing the update with an old 828mk2 instead solved my problem.

If you want to downgrade to 1.12B the file is available here: http://www.elektronauts.com/files

As for the joystick issue, calibration was not going to fix the problem. So the AK needed to be sent to the repair center in LA. My retailer (Moog Audio) was kind enough to replace my AK and take care of sending it in LA for me.