personally.. i've noticed this:
Booked a flight on USAir metal... used my AAdvantage # (which does have my GE#)... then when i go to check in online (or phone) and get boarding pass... no precheck. so i log into USAir with my COnfirm Code...NOT thorugh my USAir log in...reservation comes up with no GE #. I load the GE # in... re checkin from the USAir site... send a link to my phone... boarding pass shows up (for iPhone's wallet) with precheck...
yes it's annoying... but i want all my miles to go to AA (except when there is a promotion with USAir)