Yes both her nominations were for Navy. I think for the Senator she had to put them in order of preferance. She might of just had to pick one for the representative, so of course she put her first choice. The question is what to do at this point if anything.
I'm not following this. If she had to list her preferences for a nom and she listed USNA first, I assume she preferred USNA over USAFA. Thus, I assume that USNA is her first choice. That's why they ask.
If she got 2 noms for USNA and that was her first choice, she is in a good position to receive an appointment to USNA. Why are you worried that it won't happen?
If you wonder what she can do to receive an appointment to USAFA -- I'm not sure. If she wanted to attend USAFA, she should have listed that as her first choice. I had this happen to a candidate a couple of years ago. He picked USMA as his first choice for two MOCs and USNA for the final one. He got the USMA noms but not even an interview for USNA and no nom. He wanted to know what to do -- I told him that his first choice obviously was USMA (2/3) and he got that. He went to USMA.
Am I missing something here?