Processing time can be painfully slow. If you sent them (sure you have), USAFA will get them and process them. In the future, you may want to pay a little extra to get delivery tracking so you will have confirmation it was received. Though USAFA wants you to follow the schedule and meet the dates, if there is a SNAFU with the records, it is very likely USAFA would accept your counselor's word they were sent originally and on time if a new one is needed. (Also is faxing an option? - I seem to recall DD faxed some documents last year)
As an example of the bureaucracy - ACT/SAT scores can be delivered to schools electronically or via CD. Last year USAFA was one of the school's that received them via CD, so someone had to physically load the CD into the system which added time to the process. Eventually, they were updated in the system