Yesterday I called and requested mileage credit for AUS->DFW and did not mention anything about ending up on the single flight number (1309) 2 segment trip. I was told that the credit would show up the next day.

Today it shows:

11/09/09 AMERICAN AIRLINES 1309 Y DFW SFO 1,464 1,464 2,928
11/09/09 AMERICAN AIRLINES 1309 Y AUS DFW 183 817 1,000

So I did get credit for the individual segments instead of just AUS->SFO as if it were direct. This means with my 3352*2 mile MR to MKE I'll re-qualify for PLT by 555 miles. Sweet.

Thanks everyone for the help!
Rayfes