Right now, I've got two pharmacies. I have our local hometown pharmacy, which is good, because they're focused on their customers, and willing to order anything I need, that they don't have. I have the local Wal-Green's for the middle of the night/weekend meds that are called in. Anyways, as long as I've been getting meds for any issue, not just CF, I would rather deal with my local pharmacy then a chain one, ANY DAY! The only downside I've seen, is that sometimes they have to overnight the meds, and they don't always make it in, when they say they should.
Anyways, good luck!! I hope you can get something worked out!