Hmm, interesting. I tried the web page you linked to just now. It did have functionality for looking things up based on "document number". First for "document number" I tried the transportation voucher number. It showed the original voucher amount but nothing deducted from it. Next I tried the ticket # of the itinerary that I ticketed yesterday. In the latter case it says that all I can do is cancel the itinerary and proceed with refunding - obviously don't want to do that.
For the first search result it did give the option of sending this over to a "refund specialist" - thinking maybe I will do that (based on the voucher #) but then cite to the ticket # of the itinerary I ticketed, and explain the tax/fee situation.
You mention calling - who did you call? Just general AA customer service?