As it is the airline, the hotel, your credit card, your rental car-company etc. giving (paying) the miles, this doesn't depend on the travel-agent but on the rules of the airline/hotel etc. With UA and Swissair (and now also with LH) I know you get your miles always on paid flights (not on military and governement fares).

Some Hotels (Hilton for example) will, on consolidated rates, often only give you the minimum points (and no miles). As IAPA "just" makes the reservation (no prepaid voucher) you get in most cases credit (on prepaid-vouchers from tour-operators often not, exeption: Marriott Miles always 500 miles, even on stays with vouchers).