Thanks for answering all my questions.
I texted a vet that I work with to ask her when she would AI a dog based on progesterone levels. This is her answer "Optimum breeding time is 4-6 days after the progesterone level reaches 2ng/ml."
So it looks like you're just barely missing the time to do AI....of course, you'll have to work with your vet to make sure that you're timing the AI with the cornification of the cells. At the general practice I was in, we would attempt AI if the progesterone levels were in the neighborhood of where they were supposed to be and if the cells were at least 90% cornified.
As for the Cystorelin, I did some looking into it, and the other name it goes by is Fertagyl. I've read good and bad things on it, some people swear by it, and some people have said that it did affect the number of pups in the litter...more specifically, that it decreased the number of pups. There's more information on it here:
There's also a great website that is easy to understand about breeding based on hormones here: http://www.peteducation.com/article.cfm?c=2+2109&aid=3201 . Hopefully between the progesterone levels and the cytologies, you can get her bred.
Good luck...Bernese are amazingly beautiful dogs!!
As and edit....one of the other experts on this site pointed me to the possibility of having her tested for the canine herpes virus. It can affect a female and render her infertile, so if she hasn't been tested, it might not be a bad idea. There's a site about it here: http://www.showdogsupersite.com/kenlclub/breedvet/vhr2.html