I don't know if this helps at all but I did once encounter a situation where we switched from using an Adafruit GPS breakout board to using a Trimble chip. Things stopped working properly and we ultimately found (using a digital oscilloscope) that the default width of the PPS pulse coming from the Trimble chip was too narrow for the SBC to detect. The Trimble chip has a mechanism to adjust the width of the pulse and once that was done it worked like a champ. Not sure if this fits your situation but maybe something to look into? We were using a Beaglebone Black as our SBC, running Ubuntu. I don't recall the specific Trimble chip that was used as it wasn't my design and I was just called in to troubleshoot.