I just talked to them on the phone this afternoon, and first, I can confirm that on their computer they can see miles at the Choice end, even though you can't see them online at the Choice end ever, and only can see them if/when they get to the airline.

Anyhow, I had a weird problem where I noticed that my stays since early March had been posting 250 but not 500. I called them up, and several of the people at the other end looked into it for a number of minutes (putting me on hold) and couldn't figure out why it had happened, especially since it had "fixed itself" (ie, they could already see that a stay from last week that hadn't yet gotten to the airline had already been sent as 250+500, even though my stays from mid-March hadn't. They couldn't figure out what had happened or how to fix it otherwise, so they just issued me 2000 bulk miles.

Luckily these stays were credited to AA, not NW, so they won't affect the (mis)counting of Perkology bonuses!