How frustrating!
One of my writing pals who entered was reassigned to a different judge. She just got a letter from the contest stating that they were having some administrative issues and that if she hadn't sent it to the second judge, to email it directly to St. Martin's.
My suspicion is, there has been some shuffling or perhaps some layoffs, and the contest organizers are a bit overwhelmed. I would try sending a letter to your judge, politely explaining the situation and maybe even including a copy of your receipt as proof that you sent it by the deadline.
The good news is, you can still query agents with the manuscript you've worked so hard on.