Saeco xsmall flashing warning light issue

Hello all. I picked up 2 semi working saeco xsmall and spent several days troubleshooting and fixing both. Using the differential issues, manuals, and forums, I managed to fix them up quite well. I now have 1 fully working unit and had to buy a new pump for the second machine.

Now here comes the issue. The second machine stays stuck with the rapid flashing warning light (lines need to be primed). To be clear, I've used the working machine (#1) pump and brew unit in this machine #2 to no effect. I've used the machine in test mode and every function works properly. Water flows well, the flow sensor flashes the light appropriately, I can run water through the brew unit perfectly fine of I engage it in test mode 1 and then run the pump in test mode 3. Everything works except that when the machine is in use it never wants to acknowledge that the lines are primed! I put the machine on hot water, it primes (for about 5x longer than machine #1 needed), changes to slow red flashing (as its supposed), and when I switch it to bean, it goes back to rapid flashing.

Any ideas?

Thanks!

I just had a thought... What are the sensors used for water presence in the system? The flow meter works fine, but that's for the pump. How does it detect if the lines are primed?