Thank you both for your replies

It is the high Bb and A. Bb3, as you called it. And then the A.
She does not have a private flute teacher, but I am going to try to find one. I did a quick search for one in the area and nothing came up, but I am going to ask around. A couple of weekends ago, she was in the Honor Band at Virginia Tech and it occurred to me that I surely could find someone in the music department there that gives lessons, or at least could point me in the right direction.
That is a good idea to have someone else try her flute, and for her to try another that is known to play correctly. For what it's worth, when she was first learning those two notes a few months ago, she struggled for a little while, but it sounded different during that struggle. Kind of like it kept going down an octave. Then she learned them and all was great. This is a new problem, and it seems odd to me that it goes away after a few minutes of going at it. Maybe she is doing something different with her embouchure than she used to do.
I will definitely have to find a way to get her to try another flute. Thank you so much for your suggestions! I'm going to add a link to a video of her playing this morning, just so you can hear the type of sound that is coming out. Please excuse the fact that she was rushing. We were about to leave to get her to school. She mostly wanted to see if pressing the keys a little harder made any difference, which it didn't. And also to get the notes coming out before school because she might be having a test on scales this morning. Once she gets them coming out, it plays fine for long enough that it should be okay through Band.
http://youtu.be/_pBadTSLA_o
~Diane