After thinking about it a little I realized that it is also a tax that they refuse to collect if you want to do a Form 1, but will still punish you for not having paid the tax and getting the stamp.
They cashed the check, not issued the tax stamp. I suspect they gather checks and money orders in batches before they deposit them ahead of starting the paperwork process.
My understanding is that they only cash the check if the background investigation passes and if not the uncashed check is returned.
They can always refund the money! They just want to get their money while there is money in the account to cover the check!
In my experience they always cash the check first, now matter what the outcome and that is with 20+ tax stamps. I did have one stamp rejected due to the changes of the Trust regulations (post dated after the changes due to shop employee not mailing it off for three weeks) and never got a refund for it, however they did cash the second check and approve the suppressor the second time.