I don't know about this situation, but HOAs tend to play a little game with people. If you miss getting your payment in on time, they send you another notice for the same amount, and then quickly start tacking on more fees and penalties. When they get your check, it doesn't match the fees and penalties that keep mounting so they reject it and take their time telling you.
Short of you walking into their office and demanding a full payment amount, they can and do keep this circus going until the HOA president gets to sell your house to his brother-in-law for 1/20th its value.
Makes a pretty compelling argument for getting your payment in on time, doesn't it?