i think you just havent assigned the axis correctly, if they are registering on the horizontal bars, there is nothing wrong with the dfp itself.
Continue to play with the settings for the throttle brake combined axis. Its in there somewhere!
As an aside, the very first problem you had, the throttle not registering full on the green in game bar, i just had today. It solved it by unplugging and plugging the wheel back in at the usb plug, but a couple of times it came back. I reckon its something in the driver software thats responsible as the pedals still functioned perfectly, just didnt give full throttle??