Hi ABZ Alfa,
Have read your post and can relate to your exact problematic condition regarding the rad fan operation.
I have a ph 1 GTV 1996 Lusso, with twin fans and A/C. I have the car 6 years and have done a fair bit of work to it, some necessary and quite a lot which wasn't..! A theraputic way of spending money I suppose..! As part of this expendature, I decided to treat the car ( myself ) to a chip upgrade. When I fitted it it gave a good increase in low end performance, which was what I was looking for as I had just rebuilt the top end and had fitted a pair of Colombo & Barianni camshafts for improved low end pull at that time. After a few months I noticed that it appeared that my 2nd stage fans were not operating. As the rebulid was done in January the weather had been fairly cold for some months so I didn't really notice this too much. However as the warmer months came around I finally made some time available to research this confusing issue. I spent a long time going through circuit diagrams/ relay operations/wiring continuity checks and component operation tests to make some interesting observations.Your tests replicated mine.If you have forced both speeds on by disconnecting the temp sensor plug,the circuit is ok.My problem appeared to be that the new chip not being mapped for my ECU version M2.10.4 which controls the fan speed operation for cooling and A/C. Other ECU versions fan operations are controlled by a thermal switch fitted to the radiator. When I swapped the original chip back into the ECU and ran the engine the cooling fans operated as before ... i.e. 1st stage switching up to 2nd stage and back to 1st stage then off for a predetermined time depending on cooling requirements and the starting the cycle again. More noticable is the A/C operation where the stepping operation is most evident.So in my particular case the condition was brought on by change of chip. The operation of the 1st stage fan comes from pin no. 26 out of the ECU that of the 2nd stage fan comes from pin no.25. But if when you remove the temp sensor plug and both speeds kick in, as was the case in my car also, then one would imaging that the circuit , relays and wiring are 100%....so can your problem be internal in the ECU...especially if you are running everything in standard factory mode.
Not sure if this reply makes any sense of the problem but I hope it may give you some direction for some further investigating. Keep in touch with any updates.