Everything is working like it should except for the tailservo. The servo is "centered" in the extreme right position (output 2000 in the config program). The input from the receiver is ok, everything is centered and endpoints are adjusted correctly. Tried to connect the servo directly to the receiver and it was all ok. Tried different servos as well.

This is caused by old QUAD eeprom/flash settings getting stuck in the on-board flash area and corrupting the tricopter configuration. Go into MultiWii Config GUI, start the data rolling, then hit the RESET button which will clear out all settings.  Now your tail servo should be working properly. Reconfigure your PID and AUX settings and hit SAVE.

This is a known issue with MultiWii code, I am trying to figure out a good fix for it in software.

FYI You will need MultiWii firmware version 2.1 or above to get the RESET button, the RESET button didn't exist in version 2.0. If you don't hit SAVE after the RESET then the corrupt settings will return on the next power up!