Did your employer's travel agent perhaps purchase bulk fares or something else that's discounted and contractually isn't eligible for FF credit? Can you look at the receipts to see the fare codes on these tickets?

Is there any chance that your travel office could be using some fly-by-night (no pun intended) travel agent or mileage broker that's giving you tickets purchased with someone else's FF miles? Could they be booking some sort of cheap package "tours" and having you use only the plane ticket?