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Josh,
There is obviously some kind of chemical reaction taking place here.
I wonder if there is some type of coating on the material to protect it.
Do you have any scrap pieces left over from the construction?
If so, you might try some experimentation with them. Do some heavy cleaning on them and try to determine if this possible coating can be removed.
Regardless, until you have some concrete answers, I would not make use of the enclosure for live animals.
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