As a little follow up to this...
I have today recieved a PCN for riding my Versys through the ULEZ. This one was a warning but it promises of more to come if I don't pay the fee.
I've of course challenged this and presented them with my letter of exemption I had previously obtained.
I've heard rumors that there's been issues with their database of motorcycles as far as what is exempt and what isn't, so I'm hoping this isn't a sign of things to come!
Will keep you all posted! :-)