It was over the max daily limit for deposit through mobile deposit, for me it is $10,000. Not sure if that is standard or what. My check was also a federal state check, which USAA did warn me that depending what "type" of check it was, there could be a hold. I guess when you deposit it the system will let you know automatically if there's a hold on it or not. USAA has no control over that if you deposit it this way. I hope that helps.
Have you tried calling USAA to see what the hold up is?