Yes and no. Usually the search engines on the first pass search for fares, but not the availability of those fares. It may say there is a fare for $400 between New York and LA on XYZ airline, but it will not check to see if that fare is still available on the days and times you are looking for.

There was just another thread on Kayak doing the same thing in the past few days.

When you check the airline's site, they are actually checking to see if there are seats available before giving you the fare.

Also, if you are booking multiple tickets, say four tickets, and they come back with three left at $400 and the next lowest price of $700, they will charge you $700 for all four tickets, not three at the lower price. Always try breaking it down to 2 and 2 or each individually to see if there's a difference...