While the uC has been outputting PWM as designed, there have been other problems...
First off, when I designed the board, I based it on the "Family Reference Manual" without thinking to ensure the extensions I was using were actually available on the uC I was looking at. This led to me trying to use PWM1L independently to PWM1H, which is not supported. So I instead needed to use PWM1L and PWM2L, PWM2L is attached to one of the pins I am using for the buttons, so there was a need to switch the pins around between the uC and the board.
Secondly, I had taken the Vdd on the FET driver to mean the 3.3v rail, so the driver was not working at all, it needs over 8v to work :(
I tried to make some changes on the board with patch wires to accommodate these design errors and in the process, I managed to pull several pads off the board, and break off one of the uC legs. Even after working through these problems, the uC is no longer programmable, so there is no telling what is shorted to what :(
I came to the conclusion that I will need to order new boards to fix the problems, so I will redesign the circuit for 4 switch operation. This will improve the efficiency of the converter, and it will actually end up being less expensive, because I will be able to use FETs that are less expensive than the diodes.
I have added the extra parts to the schematic, now all I have to do is add them to the board, ideally without needing to increase its size.
*sigh* hardware is... hard!