Depending on the software in use, AA's systems will "lock" the ability to check a bag and print a label. The reason is that TSA needs a specified time to process all of the bags so that they can be timely loaded.
I am surprised that this is the case at FAT. but that is the new and spreading norm.
The fail here is that at a small station where there were no additional personnel to help, at least one of the agents ought to have stepped away from their immediate task to process bags once it came close to the deadline. To be frank, at T-55, I would have interrupted and apologetically asked whether there is anything to be done given the looming deadline.