In searching for a ticket DEL>BOS, BOS>DEL, the IATA search engine gives some pretty good fares (http://matrix.itasoftware.com)

I found the flights I wanted, verified that seats were available in the required classes via expertflyer, and then called the airline to book, but the agent said that nothing was available.

Has anyone encountered this problem before? Is this a 'bug' in IATA software (e.g., should it indicate it can't check avialability).

The routing was pretty complicated (DEL>VIE on AI (operated by OS), then VIE>LHR on OS, LHR>BOS on AA); it was an AA fare (VLRISD). Perhaps the AA computers can't find AI seats?

Would a travel agent be better at this than the airline?

Any thoughts appreciated, it would be a $600 savings...