What a horrible day this has turned out to be.
1) Discovered that for whatever reason my arm processor can’t keep up with the 115200 GPS messages at 5Hz.
2) In debugging the above, I broke of the female micro USB connector on the GPS board. I was using that for configuration. Now I will need to do that via the serial port till I can repair the board. Luckily I did not break any critical pads.
3) Went to place a Digikey order for various parts (including a new micro USB female connector) when I found out my ARM processor header board is obsolete and I can’t get anymore short of an order to Olimex overseas. Need to rethink what processor I am going to use.