This seems to be happening to me a lot lately. I booked a fare and flew last week from BOS - CAK in first via DTW (DTW - CAK was a CRJ200) and it came out to $542 when I booked it as a multi-city. The same fight when booking using the normal search was $680 in coach. Of course I booked the multi city in A.

Today I'm looking at BOS - LAS 10/26-10/30 and I get a fare of $411.20 for the 6:11pm flight to JFK (DL 1671) and then onto Vegas on DL 1729 on a Q fare. Returning on DL 4335 and DL 1210 (L Fare) via SLC. When I look at the same flights using the multi city serach I get a price of $331.20 all on L fares. I see the same thing via DTW (although less of a $ difference in price)for the late night flight. DL really needs to fix their website. I don't trust anything I see coming out of there anymore and always search via multi-city or one way fares.

It's to the point where it seems pretty deceptive to me since I see this happening almost every flight I book. My last two flights would have made DL an extra $220 if I had just booked them normally through their search function.