Without knowing how far in she read, I'm not sure if I have a problem throughout the book, or if the problem is in my initial chapters and she treated the full as a partial and just gave up. Surely, if she couldn't connect, she wouldn't have read the entire manuscript anyway, right?
Maybe it was just that agent. Send it out again and see, just in case. If no one says yes, then it doesn't matter how far they read, because you have a problem that has to be fixed.
Imagine you're browsing in a bookstore. You're intrigued enough to pick up a book and start browsing its first chapter. While you admire the author's background and technique, it just doesn't grab you. It doesn't connect. What do you do? You close the book and put it back on the shelf.
This is reality, as basic as gravity. Readers only care about what you're going to do for them. If you don't connect, they stop reading.
Let's assume you send your book out some more, but no one says yes. What should you assume is the matter with it? I don't know. What I do know is that all of the components of fiction -- plot, character, setting, etc. -- have to work together like the parts of a machine. By that, I don't just mean they have to work together smoothly, though they do. I mean they have interacting and interdependent functions like machine parts, and if they aren't linking up properly, your book is not going to work.
(A useful rule of thumb: if readers say there's a problem with your book, they may not be able to describe precisely what it is, or tell you how to fix it, but they're right about there being a problem.)
(Unless they're completely inept readers, of course. That does happen, but it shouldn't be your first hypothesis.)
If readers experience whatever-it-is as an inability to connect with your characters, something basic is not working properly. It's possible that you're only getting it wrong in your first few chapters. If so, that will have to be fixed -- not a negotiable issue -- but it'll take less work than rewriting the whole thing, or setting it aside and writing another, which is what you'll otherwise be looking at.
So. Send it out some more and see what happens.