Lot of flaming on forums those days about new 3DR OTP policy on mission planner.
To summarize the story, now you can't upgrade your pixhawk clone firmware from Mission Planner anymore. You will get an "OTP error" when trying to upload.
Only legit boards from 3DR works.
Considering this is an open source hardware & software, I don't get the move here.
Anyway, don't cry, there's an easy way to remove your pain.
You can upgrade your board using QUpgrade tool.

Off course, for whatever reason, all qupgrade binaries have been removed from 3DR/PIX4 website.
You can still find the source from github here.
This compiles with QTeditor.
I've compiled a windows & mac binaries here: QUpgrade tool
With all the fuzz on this, I think they will change their position and make the things different quickly.
Usage:
In home screen select correct firmware and hit Flash Now button:
FIXED:
To manually download & flash other builds follow this:

scroll down to All APM Firmware Options

go to stable or latest for current dev branch

Choose correct firmware

Most clones are v2

If not unplug it click ok, plug again.