Indoor hot tubs are just a bad idea. Seriously, even with the goings-on in that tub, keeping the water in the tub safe and sanitary is trivial with modern treatment systems (especially with a salt system). The problem you get is all the water vapor that gets in the air goes *somewhere* and generally condenses out on a cold surface. Since it is inside in this case, that cold surface is typically also inside the house, and the the water causes all kinds of science projects, wood rot, etc.
Designing indoor spaces for pools and hot tubs is a non-trivial undertaking. At least if you want to do it right.
I think the problem was not wood rotting, but wood sprouting. :O)