How were the GPs tested? (I generally do a simple ohm test and it's been reliable enough for me, but many folks swear that you have to actually apply a load to them to test.)
If you pop off the connection on the GPs what happens when you go to start? It would be nice if you could trigger a code and see that you've done so. Really just looking to see what logic is happening.
I'm assuming that the ground for the GPs is good. Not sure how it would show up if not.
My MKIV VW TDIs rely on temperature sensors to determine if they need to operate. On manual cars they even have GPs for the cooling system: coolant GPs. Not sure of the full circuit logic on these. I DO know that unplugging temperature sensors can help in forcing GPs to operate: it's a default mode. And the coolant temperature sensor has two circuits, one that feeds the ECU and one that feeds the dash gauge; each circuit has the ability to act up- usually it's the circuit to the gauge, causes the gauge to go wacky, but the circuit to the ECU is fine and the engine therefore runs w/o issue: I have a multi-gauge plugged into my ODBII port for providing a bunch of readouts and can see the temps reported to/by the ECU (no panic if the dash gauge shows bad stuff is happening!).
Regarding ECU and operation, something like GPs isn't going to be part of any no-start logic (though, in reality, when not working, they can cause your engine to not start

). GPs are mostly emissions related stuff: in my TDIs pretty much just failures of emissions stuff will trigger standard ODBII codes: VW will log other stuff that's proprietary, but GPs ain't in this set.
If it ever came down to it one could install a timer circuit that would put the necessary resistance on the relay [served/controlled by the ECU] that drives the GPs, do this when adding on a manual circuit to do the actual activation of the GPs.
As has been noted, the connections to/from the ECU can be a suspect: many harness connections are less than stellar at keeping out moisture: though possible that only one pin (for GP circuit) could be problematic I'm thinking that this would be kind of rare, a possibility, but less probable. If nothing else it can be considered as a preventative maintenance measure. Clean it all up with
DeoxIT.