I have a mortgage with B of A also, and I know firsthand what the source of confusion is. For a period of time, I was also making extra principal payments a couple weeks after the actual due date, and the first time I did it, I also noticed that the entire amount wasn't deducted from the principal. But it actually all works out in the end. Here's what happens.
Let's say that your mortgage payment is due on the 1st of the month, and your monthly payment is $1000. Some of this goes to the principal, and some goes to interest. Once the appropriate amount has been deducted from your principal balance, interest starts to accrue immediately on the remaining balance.
On the 15th, you send in an extra payment of $200. However, interest has been accruing until that point, and payments always go to satisfy interest before principal. So instead of your principal balance going down by $200, it only goes down by $50, with $150 going towards the interest. Doesn't seem fair, right?
But then this is what happens when you make your next monthly payment. When you send in your regular monthly $1000 payment, half of the month's interest has already been paid - the $150 of your extra payment. Thus, a greater proportion of your regular payment goes to pay down your principal. So instead of $300 going to interest and $700 going to principal, for example, $850 of your regular monthly payment goes to principal.
So it all evens out in the end. I, too, called B of A in a dander when my first extra payment didn't get properly applied (or so I thought), but this was explained to me. I watched my principal balance like a hawk for the next few months, and indeed, my principal was being paid down as expected. I kept a detailed amortization calendar to confirm this.
Try to find an amortization calculator that allows for extra payments (bankrate.com has a good one) and see whether things are working out correctly. In my case, every single penny of my extra payments went to pay down my principal faster.
