As posted here yesterday:
http://www.flyertalk.com/forum/showthread.php?t=458487
Depending on how the fares map, you may run into problems in the following situation: UA flight number, AC is the operating carrier, points credited to AE.
If it is a UA flight #, and UA metal (including TED, and UAX) you will receive full points.
According to others, the fare mapping varies depending on the route.