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One of two things. Since you already have the plaster, try to finish what you are doing with the plaster, but let it totally harden for an hour or so. Then, put a light coat over the teeth on the plaster of vaseline, then attempt to use the trays, and don't overheat them. You may be overheating them...?
If the above does not work, but it hopefully will work. Try this as a second choice - Use Dental stone, as opposed to plaster. Stone is harder, and will not tend to discolor. You can use golden brown, blue, green or white stone, they should all work fine, and I've personally never had them leave any color or residue behind. I'm sure one, if not both of the above techniques will work for you...
*Please let me know if I can be of any additional assistance - OK?
Does the above make sense?
Let me know if questions linger...