Yep, I almost always book directly through the airline after getting a rough idea of what flights are available through one of the big search sites. My wife "saved some time" booking through a search site earlier this year and after a couple months we got an email that our flight had been canceled and their solution was to rebook the outbound leg two days earlier... um. NO.
Luckily they gave a full refund and I rebooked directly with LH. Cost about 25% more and an hour on the phone but seat reservations were "free" the second time around.