A lot of strange stuff here. As already pointed out, it is against AA's stated policy to sell kiosk upgrades when there are elites waitlisted. (Not so YUP and KUP.) A GA not knowing a pax status - B.S. - although they may not feel at liberty to confirm any others pax's status to you. As for PLT clearing a sticker "X" FOUR DAYS ago - impossible, in theory, with a 72 hour window - but an "A" upgrade - miles or vip (CAN happen for a PLT - 2 MM, friend etc) - can certainly clear at 4 or 40 days out - well before your sticker. No where did I see you reference the booking code of the PLT - only your own - so perhaps possible? And finally, maybe your "through" flights requirement for upgrades on both segments allowed a PLT on the UPG list to process at 72 hours for the second segment only - it could happen within the rules a I understand them - "X" opens segment by segment - and if your second segment was holding tied to the first...

Just thoughts...

Also, you have a boarding card that the PNR says never happened -VERY strange....