**SOLVED**
After messing around with various ideas for quite a few hours and mainly looking in the area of something to do with the boot release system I've traced it down to my after-market roof module. Once I removed that, and that's not easy when you can't put the roof in service mode, it worked perfectly in fact instantly as I'd left the two boot catches in the closed position but it wasn't drawing it in (boot in fully open position) so as soon as I'd put the loom plug back in place the boot motors drew it in, pressed the boot release catch and it released as it should.
So no microswitches, or hall sensors required, just either a replacement or deletion of the roof module. Not sure if I want another module fitted really as if it's going to be this unreliable then I'll "cope" without one as I'm simply not justifying £340 for the SmartTop version, it hasn't got that many benefits!
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