This is still an issue - received email to check in on line and a few hours later, a confirmation email that my room was ready. When I arrived at the hotel, they checked in the system and even though keys were ready for me the system did not show me as checked into the hotel.

I thought perhaps the system was down last week to address the issue as I did not receive an email inviting me to check in online but it looks like this was not the case. The property is going to follow up again with corporate but this sure is an interesting quirk.