Hmmm.. two things I can think of...
One is to claim directly on your upstairs neightbours policy... I know it's also your policy but you are claiming under his name and so he is liable for the excess... I know for accidental fires you cannot claim from your neighbours policy, but is this true for floods? What I mean is.. if this happened in two semi-detached houses you may be able to claim under your neighbours policy, not in the case of a fire due to the Accidental Fires Act.. but probably in the case of flooding.. so attempt to do the same here..
If this isn't possible then consider suing the owner directly, for your loss due to his negligience.. Ok, he may not have been negligient, but neither were you, and you have suffered a loss due to his problem, so sue him personally... firstly of course ask him nicely to pay, if he refuses send a solicitors letter stating you'll be suing, and you'll be charging all costs to him.
I think it's a disgrace if you are out of pocket and the owner causing the problem gets off scot free!!!!
What would happen if the same thing happened in two semi-detached houses?
I think the government needs to start 'governing' in relation to apartments, management companies, developers not handing over shared land, councils not taking estates in charge and imposing illegal planning conditions.. etc etc...