So they weren't really concerned with getting you reimbursed, but sure are concerned about getting themselves reimbursed.
Talk to your bank. From your posting it looks like you deposited that check on the 12th. If they got that stop payment issued on Friday the 14th the deposit you made could come back resulting in bank fees for you. Add that to the fee they have to pay for the stop payment and it's really gotten out of hand. I can see them freaking out a bit, but assuming you have worked for them before and you were proactive in contacting them instead of waiting for them to catch the mistake, the company causing all these headaches and ultimately costing you money is totally uncalled for.
I would contact this guy immediately. First, tell him you are not issuing a check until it is certain his bank did not return the first. Second, make sure he understands, in no uncertain terms, if that check is returned you expect a replacement within the week. And, lastly, if your bank charges you any fees you are holding them responsible for payment.
Equal rights for others does not mean fewer rights for you. It's not pie.
"I prefer someone who burns the flag and then wraps themselves up in the Constitution over someone who burns the Constitution and then wraps themselves up in the flag." -Molly Ivins
Never try to teach a pig to sing. It's a waste of your time and it really annoys the pig.