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@Gordon
Great, thank you!
I believe we have found the issue. At startup the GPS enable pin wasn't being set one way or the other (it was left 'floating').
This never used to be a problem as the GPS defaulted to being off, but it appears that in the most recent boards a new batch of GPS chips have been used (although they report themselves as being identical) and somehow this has meant that some of the GPS chips now turn on when the enable pin is left floating (although not always!).
I've just updated the firmware, so if you now install the latest 'cutting edge' firmware the GPS enable isn't left floating but is solidly turned off, and this should completely fix the issue for you.
Thanks for bearing with me on this - but hopefully this'll fix your issues once and for all!