Airlines and hotels often have agreements with the aggregators that they will not offer fares lower than what they are making available through the GDS aggregators.
This is why hotel sites will offer discounted prices based either on prepayment, or package deals, so that the price isn't directly comparable to Expedia, etc. It's also why those deals are sometimes the best - with sites like Expedia/Travelocity taking something like 30-40% of the nightly rate (versus a much lower % for airline tickets), hotels should be willing to bend over backwards to get you to book directly.
Also, it's possible to put a hold on a ticket without buying it; I'm guessing here, but if you're looking at one system the available fares list might reflect that some seats are on hold (by not showing those fares), while another system might not, resulting in different fares being visible... that will generally show up as a difference in the lowest-priced fare, since most of the search sites highlight that parameter when displaying search results.
I'm also scratching my head as to why we're now ~3 (maybe 4 counting ITA?) levels deep for purchasing of airline tickets? Hipmunk -> Orbitz -> ITA -> Airline
There is a lot of "slack" in how travel is priced due to all kinds of agreements about what rates you're allowed to show. That's partly why package deals can be so good. These are not simple problems to solve, even in a best-case scenario.
This is why hotel sites will offer discounted prices based either on prepayment, or package deals, so that the price isn't directly comparable to Expedia, etc. It's also why those deals are sometimes the best - with sites like Expedia/Travelocity taking something like 30-40% of the nightly rate (versus a much lower % for airline tickets), hotels should be willing to bend over backwards to get you to book directly.
Also, it's possible to put a hold on a ticket without buying it; I'm guessing here, but if you're looking at one system the available fares list might reflect that some seats are on hold (by not showing those fares), while another system might not, resulting in different fares being visible... that will generally show up as a difference in the lowest-priced fare, since most of the search sites highlight that parameter when displaying search results.