I just spent quite a while dealing with what I thought was a receiver or Pixhawk hardware failure on a homebuilt quad. During debugging, I wanted to refresh the Pixhawk software and parameters so I checked this forum for a how-to. The recommended solution was to set up the Pixhawk as a plane using the wizard, then re-set it by re-running the wizard setting it up as a quad. I ended up with what looked like an inability to store ESC calibration values on the pixhawk and some other weird characteristics.
Eventually I eliminated the receiver as the problem but just to be sure, I went back to a known good receiver that had worked properly before with both an old APM and my new Pixhawk. The problems persisted and debugging continued.
Eventually, I will spare you the saga, I noticed in config/tuning mode - full parameter list menu that the parameter file referenced in the drop down was something like 3DR_AERO which did not seem right. I changed it to 3DR_quad_RTF and then reset to factory default.
Problem Solved!! It looks like either I or MP did something that caused it to not use quad parameters and to use AERO parameters. I hope this helps others as I was getting really frustrated after hours and hours of plugging, unplugging, battery connection, recalibration, changing parameters, calling 3DR, etc. etc. 