Man, just had a very similar experience with PenFed. I was looking forward to working with them since they now have a 6-mo intro rate of .99% and 4.25% for the HELOC ongoing. My 3-flat did not qualify for a desk or drive-by appraisal, so they sent out someone (at cost of $705 to me) to do a walkthrough, and the appraisal came back about $13k lower than my recent refinance. Not the end of the world, but I was really surprised at some of the comps and evaluation standards that were quite different than the refinance appraiser submitted.
Long story short... I went back and forth with PenFed on what I considered factual errors, but the appraiser refused to budge and the PenFed appraisal desk ultimately supported him.
I was hoping to access 90% LTV ...about $50k in equity but now will only be able to access about $40k.
I don't want to go through the whole process again with another lender though...bother my tenants, have a hard credit pull, and run the risk of potentially another appraisal wildcard.
I guess it's just part of the game, but sure wish there was a more standardized approach in the appraisal industry.