My guy's cage has an odd smell too, I think it's the plant soil, cos it doesn't go when I clean out the poop. & it doesn't really smell if the poo get soggy... But to be fair, he also likes to hide his poo...so there maybe some that I haven't found yet. I need to take the ficus out for a clean.
I'm not sure how to resolve drainage issues with plants, I think some people put gravel at the bottom of the pot.