I'm having a similar problem. My SO keeps going back and forth between saying he'll apply to transfer (undergrad) to the same school that I end up at, and saying he wants to stay where we are right now (and we just wouldn't be together). We've been together for a very long time, so I don't want to leave him, but I don't want him to be unhappy if he comes with me, either. I don't think he's ready to leave where we live now, but for me there is no other option if I want to go to grad school (there aren't any schools I'm even remotely interested in where we live presently), and I pretty much have to if I want a decent job in my field.
It's so incredibly frustrating, but the more I try to talk to him about it, the more frustrating it is because he won't make up his mind.