This reminded me of a horror story I read on someone's blog a long time ago. It was during the real estate boom, and most likely couldn't happen today. The blogger had gone through her builder's preferred lender and they ended up messing up somehow and were talking about missing the closing date. Her contract with the builder stated that the negotiated price was only good until the proposed closing date. If they had missed the date, she'd still be able to buy the house, but only at its NEW price, which would be several thousand dollars more (she knew of one buyer who actually did have to reschedule closing, due to the same lender, and ended up paying $40K more). So, like I said, this particular scenario probably couldn't happen today. But it does demonstrate that the preferred builder is not necessary competent or honest. I'd get good faith estimates from other lenders as well - like a previous poster said, you may actually get a better deal.
Forgot to mention... we didn't use a realtor when we bought from the builder.