To get from point A to point C, there are no direct flights. Must connect at B.

From A to B fare class S is available on flight 1 (S9)
From B to C fare class S is available on flight 2 (S9)

From A to C, fare class S is not available on flight 1 connecting to flight 2 (S0)

All the rules met, S fare is published for all the cities, B is valid connecting city etc.

I thought that is S was available for AtoB and BtoC, S would be available to go from A to C connecting through B. Obviously thought wrong, and wondering if someone could explain this....

Also appears to me that Flexible Date Search prices using fare classes available on individual legs as opposed to the trip, and will show a low price based upon that availability; but, when you click through to select the flight, if that class isn't available in the "hidden" A-to-C via B bucket, the website wants to reprice higher. (Also appears that web support, upon verifying the website prices it out a lower price, will honor the lower fare, but will book it into a higher fare bucket. Can work out very nicely if you get charged the 'W' fare, but get ticketed in 'B' on an int'l itinerary which then allows you to upgrade with a piddly amount of miles......)