Had a similar problem with a bank way back before direct deposit was invented. I deposited my paycheck (a US Govt payroll check) and about a week or so later, I had Insufficient Funds notices coming in from everywhere! By my calculations I still had several hundred bucks in my account. Trip to the bank showed they had no record of my deposit. While complaining to some manager, a bank VP who happened to be walking by overheard us and stopped to see what was up. She then stated she had that check in her in-box on her desk. We went up and there it was, in a plastic envelope with the attached deposit slip. She had no idea why it was there and did not know what to do with it. I stated that the deposit slip (which was properly filled out) might have been a clue! The bank contacted all the business' that I had bounced checks to and explained the problem was the banks and they also took care of the bounced check charges. Checks were resubmitted and all was ok.
That being said, I think banks do have a policy where deposits made one day MIGHT not be credited to your account until the next business day. This is usually posted somewhere, like the front door or drive up window. This may be what snagged you. Hope that was not the case and if not, the bank should contact your Progressive agent and try to make it right. I have Progressive on both my bikes.
Of course my incident was over 30 years ago when customers were still people and not just account numbers.