This is a good presentation about the complexities in creating and pricing itineraries:
http://www.demarcken.org/carl/papers/ITA-software-travel-com...
Most companies don't want to take on this complexity, so they outsource it. The companies that provide this service, like ITA, tend to charge more money for more expensive queries, like multi-day searches, so most online search companies will only let you do the cheaper kinds of searches.