Progress has been slow but I do have an update.
After making about 5 boards using the Silicon Labs PoE chip I'm convinced either there is a fault with my batch of chips or my QFN soldering isn't up to scratch as I can only get 1 board to work reliably (the board I developed all the code posted here).
So back to the drawing board and this time I decided to use TI's PoE solutions as I find Ti has better documentation and an active forum (better than other silicon manufacturers), and Ti have a very good range and easy to find. So giving up the fully integrated PoE chip from Silicon Labs and using the TPS23750 from TI, which is TTSOP so no mucking around with soldering QFN and PoE AF which is enough power for this sensor platform and has an integrated switcher although requires external diode bridge and MOSFET. So with some re-jigging with KICAD I got the new PoE solution on the 50x50mm PCB, and swapped for a cheaper switcher MCP1661 to boost from 3.3v to 5v or 12v to power the sensor.
So the overall design is pretty much the same just with different chips, and this time my prototype works first time (after fiddling with the compensation circuit as the switcher was cycling on / off initially) and thanks to Ti there are a number of reference designs so I used the 3.3v 0.6a buck which is designed for IP cameras (see PMP5592 and svlrar9.pdf for the details). Also gave me the chance to redo some of the PCB layout that wasn't quite right previously (eg. all large components on the rear side of the board for better mounting - upside down).
After a bit of rejigging some of the PIC code snippits I have posted about earlier, I have OLED, ultrasound sensor and Ethernet with MQTT communicating to my home automation server. I'll post the KICAD schematics / PCB and mplab C code to my GitHub page for those who want to have a closer look.