She should be pretty much finished with teething by now, but it's possible that it's still going.
I would be very surprised if that's the cause though. Dogs don't normally whimper in pain - they whine/whimper when they want something. It is an attention-getting gesture. And since your girl is just entering her adolescent stage, I'm even more inclined to think that's the cause.
How do you react when she whimpers? If you suspected pain, then I'd be willing to bet that you've given her attention for it (that's not a criticism, btw). But she'll have learned straight away that whining gets her attention
If you really think some sort of pain could be the cause, then you should have her checked out by a vet. But if there's nothing wrong, or the idea that something could be causing her pain was just that you couldn't see another possible reason, then I'd assume the cause to be attention-seeking and put an end to it.
I'd suggest that you ignore it (and her) completely when she does that. Even get up and leave the room. Since that isn't what she wants to achieve, she will learn that whining doesn't actually work at all and give it up. Not instantly, of course, because it's been successful so far and it will take time to convince her that the technique no longer works. But unless you want to have a permanently whiny dog, I'd suggest you nip it in the bud now.