Thanks for all the kind responses.
In better light I have seen that they got over my back fence. There is some communal ground for flats at the back of my flat and they've managed to get over that somehow. In the light I was able to see where a plant had been squashed. I was surprised as the bike is pretty heavy (it's got a front suspension fork) and the fence is over 6ft with trees and shrubs, which I thought would make it nearly impossible to get a bike over it!
AMFM - I'm looking into getting one of those metal bike sheds with multiple padlock points. Although I'm tempted to just keep any bike I get in the flat from now on!
PaulR - I only had my bike on the house insurance which does not cover it that well (does not cover the lights etc at all!). Since then I've looked at specific bike insurance; the Evans one looks quite good and works out about £70 for the year with 3rd party liabilty. It covers it so long as it's locked to a fixed point with an approved lock - might be worth a look(?)