Just an update folks. This afternoon I removed the top box to access the trailer wiring and, to my surprise, found that this was wired directly into the existing loom. No isolation relays etc.. I have now disconnected this completely but the problem still remains. I have noticed that just the side saddlebag lights illuminate when the ignition key is turned to the first position, extinguish at the next position and then illuminate again with all the other lighting at the next position. This is a Canadian spec machine but I have to say I have never noticed if this was occurring previously."Removing the top box" is not as easy as it sounds. As suggested above, I would take out the half dozen screws and remove the bottom cover from the trunk - it encircles the trunk and pannier latches. That's going to give an idea of what's been messed with. Also above, the small cover covers on the bottom rear of the panniers may hide some surprises.
No one has mentioned checking the starter button. Known to get sticky and cause starter and headlight issues.
I will investigate further tomorrow. Firstly, I will take the battery to my friend at our local car spares shop and get him to put the 'drop tester' across it. If all is well I'll start checking further and carry out some of the test suggestions that have been made.