Here's something that the HUD Handbook (4150.2) has to say about log homes:
"4-4 UNIQUE PROPERTY APPRAISALS
Appraisers are sometimes faced with unique properties: a log home, an extra small home, lower than normal ceiling heights, etc. Eligibility of these properties depends on whether or not the property is structurally sound and readily marketable. If a property meets these criteria, the appraiser estimates market value. However, depending on the uniqueness of a property, the final determination to accept or reject the property is made by the lending institution's underwriter."
I went through the same thing with a perfectly good loan on a log home too --and on an FHA loan, no less-- no comps. The way the story goes is that if there are no comps, it's not readily marketable....... The lender in question had no problem with log homes in general --many others just say "no log homes" as a rule-- they just wanted comps. The only other log home that sold recently was one county over and had a purchase price significantly lower than my borrower's.