There is a problem that I know about which is that the AsiaMiles computer attempts to validate all mileage credit received from AA against what it (the AM computer) thinks is AA's route network, and if the route you are trying to claim miles for is not known to the AsiaMiles system then it will silently bounce the request. This is only a good idea if the AsiaMiles computer is very frequently updated with AA's route network, and, a year or two ago this wasn't happening.

I had this problem repeatedly after AA introduced JFK-PHX. I could only get the miles on AsiaMiles by manually requesting them.

The way to check whether this is the problem is to try to submit the Missing Mileage claim online at the AsiaMiles site - if the route is not in it's database then it will throw an error there too.

What route is it that you have problems with?