Was trying to duplicate a colleague's itinerary and entered each segment individually because the HNL-BWI, BWI-SAN, LAX-SFO-HNL schedule & price option was not matching her fare of $810. Entering each of the 6 segments individually got a lower price--$780--same dates and flights. Tried it again, and same thing happened. Any explanations?

Or, can someone direct me to a thread where this is explained? I haven't figured out the search options.
Also, if the S fare is available for all segments, why does .bomb return two segments in W fare? In above, we really wanted to go in/out of DCA instead of BWI, but it changed to W fare even though S is available, and price is $1k+.