You're going to laugh... but I use Hot Glue. A simple glue gun. It works wonderfully, is fully water resistant, totally non toxic, and dries instantly so no waiting period.
And it lasts. My current snake cages have been in use for about 4 years now, I believe, and the seals are still just fine. And even if they did come loose or flake off, replacing them is a snap and very cheap.
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