I have a feeling it's a combination of crate placement, and spending too much time in the crate.
You say that he is in the crate for 6 hours during the day? and then how much time at night?
The basement is not the place for a crate.
It's too isolated, and often basements are humid and damp.
I know that ours needs a dehumidifier going at this time of the year or it gets damp and stinky.
Bring the crate upstairs, give him a bath, wash out the crate and any bedding you keep in it and then see what happens with the smell.
Gina