I am 99% sure it is the fare class what makes the different. Webjet is not showing the class but definitely it is one of the cheap economy classes where the ticket is non-refundable and not flexible and maybe this kind of ticket is not adding much to FF program status, also you may not get the seat if it was overbooked. The class shown for SWISS
YWFFEO is a
Y class which means a Full fare class or premium economy, usually this means you can change the flight times for small fee or no fee and you can get refunded if you cancelled, plus extra miles for the FF program (if available).
Why only some agents are offering this class? because these seats are bought in bulk by these agents in advance (cheap prices) and they are reselling them. These seats are high risk investment that's why the prices are cheap but not refundable or anything. For the airlines, these seats are already sold whether you come or not. This is called consolidated tickets. To read more about this, check this page on wikitravel.