Who at AA did you speak to? I can not make much sense of what they told you, because your ticket should not require a re-issue. As long as there is availability in D for your flight, you're entitled to fly. And why AA would want to see the MRU-JNB boarding pass is beyond me. I wonder whether the AA agent you spoke to actually had a clue...

Be aware that a reissue of an xONEx ticket can be very a long and painful affair.