Be careful when booking through third-party engines to make sure you're booking the same fare code as the airline's web site does (or at least a fare code you can live with). Sometimes the third-party engines get "consolidator" fares which can be lower but which may sometimes not qualify for earning miles or not qualify for earning status miles or not qualify for upgrades.

These "consolidator" fares may, in turn, have lower fees simply because they were bought in bulk weeks or months earlier, when the fees might have been lower.