That would be what I expect. The LiFePO4 batts have much higher internal DC resistance. Considering they come off the charger at 3.6V and are 3.2V nominal, that's a big drop. Assuming nominal voltage, that's a 1.2 volt drop at 2.5A which implies ~500mΩ. That would be ~250mΩ per battery which is even higher than a NiMH batt. An ICO 18650 has around 50mΩ internal DC resistance. An IMR 18650 has around 25mΩ
Oh, and BTW, if using the 1.6Ω dual coils, I calculate 1.6V sag with the LiFePO4 batts and the numbers above. That would be 4.8V on the cartomizer. Like I said, not a whole lot more voltage than the 17670 the Prodigy also takes. Plus, the 17670 has much higher energy density and wastes a lot less power internally so you get much longer run times.