Update: Got a call from the dealers early this morning to say my new ZFE was in - hooray!!!
The guy then told me I'd have to reassemble my bike with the old knackered ZFE installed, ride it to the dealership (or trailer it) to have the old info sucked out of it, then have the technicians put a new ZFE on my bike and then download the correct info on to it - booooo!!
Alternator test revealed everything in good order, so I went to the dealers this afternoon in the knowledge that I did everything I could to narrow the problem down.
At the dealership the technician plugged my bike in to the BMW computer and said that the ZFE was indeed toast, but after downloading the software from the old ZFE into the new one there were still problems with lights and the brake light. Anyway, they sent me home on a brand new RTLC and said they'd troubleshoot the problems tomorrow and hopefully get to the bottom of things. I asked about a goodwill gesture from BMW as it was a youngish bike with low miles and in VGC with a FSH, but the parts guy seemed less than enthusiastic about the idea. I'll let you know the results tomorrow hopefully.