VRS (2.0 TSi) - Having a new inlet manifold installed (under warranty).

I'd had my FL VRS for exactly 1 month (and 3,000 miles) when the EML came on. I booked it into Skoda Manchester as they were the closest for inspection. They came back to say the fault was indicated to be a problem in the wiring loom to the ECU and that they would need to investigate further, as well as the £49 to plug it in they then wanted £250 for a few hours inspection to diagnose the problem in more detail, the subsequent repair would then be an extra charge depending on what it was. As it was wiring related they said it was not covered by the used Skoda warranty and that I should return it to the supplying dealer (who are down South). Skoda Manchester said if they had supplied the car they would sort it as part of the warranty, I therefore contacted the supplying dealer and they agreed to take it in which has been a bit of ball ache in getting the car there (400 mile round trip) and the Citigo they've given me isn't great :(

Anyway I rang yesterday and they told me that they had to drive the car round for 3 days as the EML had gone out by the time they got to it (it has been intermittently on/off). They said they had found the fault to be the inlet manifold and that they were replacing it under the warranty, which I can't fault at all.

My query is why would Skoda Manchester diagnose it as a wiring fault, is the inlet manifold anything to do with the ECU wiring or have I potentially got 2 problems? I had noted to them as well that the OBC resets itself randomly quite a lot without me doing anything to it, again I thought this could have been a wiring issue which they agreed with.