So the problem continues with the Pi 3 that is my prototype unit. The ONLY difference between it and my other RPi is that it carries a CAN bus module on its GPIO. The CAN bus module does not use any conflicting GPIO pins however it is pulling power from the Pi. I am using a 2.5Amp PS. I also want to note that yesterday I took the two modules on a road trip (grocery store) and they both got a fix and performed equally on the trip. The PS in the vehicle is actually rated slightly lower I think. Confirmed. Vehicle PS is 2.4Amp rating. Looking at config files now to see what might be different. It must be something to do with the mcp2515-can0 being active with the card sitting atop the pi because they both have the settings for the MCP2515 controller in the config.
Removing the card to see if that makes a difference. The MCP2515 Controller using Ethernet for communications. I don't see why this would cause an issue with the GPS module? Will post results shortly.