Dealer 'diagnostics'

Girl here at work bought privately a 106 1.4L petrol recently. Couple of
weeks ago, it wouldn't start at all. Main dealers diagnosed ECU failure and
recommended a new coil pack too (apparently the coil packs die and take out
the ECU). Dealers wanted ~£600 for an ECU so she got one from ATP
Electronics for ~£180. Dealers fitted it and got the car alive but then they
can't switch off the engine! They've pissed about for a week running up a
nice fat bill for >£500 on 'diagnostics' and their solution? Oh, we pulled
this wire out of this connector and it now turns off using the ignition key
as it should!"
As the new ECU was a direct identical replacement for the original, why all
of a sudden would the engine not switch off using the key?
Is there another 'master relay' (VSI?) somewhere which could have been the
original
cause of this problem? Any wiring diagrams on the Net anywhere?
Thanks for any advice.

JB