My problem was that in my alert email I had not changed the tokens (reply to email, from email, etc) to match my companies tokens. I'm not sure that will fix your issue but you may want to double check that?
I just had this same issue, the alert was working just fine and then all of a sudden it stopped.
The issue was that I had added a recipient to the alert and typed their email incorrectly (without the @___.com). Once I fixed their email it worked like a charm.