after all this rain I have seemed to have a puddle forming just behing the passenger front seats. It has reappeared after cleaning it up yesterday.

Doesn't see to be dripping from the door.

Are there any bungs in the floor pan that could come loose?

I have had a puddle forming in the drivers side rear footwell over this rainy period. After stripping the scuttle panel apart and checking the drain holes etc in the engine bay, i eventually found that someone had removed the door membrane, which was letting all water that entered the door drip straight in the car :(

Only good thing was i've just ordered a new membrane from skoda..... £3.97 inc Vat

Is this the thin clear plastic thing, or the stronger metalic looking one?

Could be that the push-fit connector for the water to the rear wash/wipe has come apart if the footwell behind the passenger seat has water in it (certainly for the Fabia; don't know about the Octy). You can tell if it's this because the jet for the water won't be as strong, and there will be a slight delay between pulling the stalk and the water coming out.

If yours is a Fabia, you need to flip up the rear seat base, fold forward the seat, and remove the plastic trim that's just inside the door opening (it just pops off). The water goes through the black pipe (which is maybe 3mm across), and the connector is near where the pipe and wires go under the rear speakers. All you need to do is push the two ends back together, and soak up the mess in your footwell with some old newspaper.

I imagine something similar applies for the Octy - HTH