Silly question, but are you sure its the floor that still stinks? I know at the shelter to get rid of the smell, we also wipe down the walls and baseboards etc as well as the floor as the urine smell sticks to it in th air.
We just use plain bleach too, but sometimes strong vinegar if its bad.
I have also heard of putting lumps of charcoal in the room to absorb the smell (but not sure if this works or not)
If all else fails, perhaps a good cleaning and then treating the floor with some kind of sealant?