Batteries that old with some use on them will loose a significant amount of their capacity, and the VTC4 is only 2100 mAh to begin with so it's possible you're only dealing with half that capacity right now (if that)
Another thing to take into account is that a regulated device keeps the power level constant, where as a mech will put out less power as the battery runs down. As the internal battery drains the IPV puts an even larger load onto the battery to account for the lower voltage, so as time goes on your pulling more and more energy from your battery.
I believe the chip cuts off a low battery when the voltage under load reaches a certain point, so when your battery is drained pretty low having an even larger load put on it to produce to same power drops the under-load voltage low enough that the chip cuts it off.
Short answer, you're probably getting more life with your mech because the total energy being used is spread out over more puffs, as each puff is weaker than the last. Where as with your IPV your getting fewer total puffs (run time) because it maintains the power over the whole life of the battery.