Sounds like you shouldn't be drawing too many amps, maybe you have something going on with the wiring causing a problem?
But you said the last flight went faster, so I guess you made an adjustment to the rpm with the timer? Either that or you changed up the props to a higher pitch?
At any rate, I would take advantage of the CC ESC capabilities and try to get the read from the flights in question.
OR go old school and hook up a what meter and see what amps you are drawing. But the ESC read during flight is way better, since it give you what was happening in the air, not on the ground.
In theory, if you only got 3 minutes of run time and you depleted the battery, you are drawing more amps than normal. Just using basic math, 25A draw should get you about 6 minutes run if you drained the battery completely. I can't imagine you drawing the 45A or so that the 3 minutes would indicate. If so, you have a problem, I would think...
You might want to see if your timing settings and such programed to the ESC are the same as what other folks without trouble are running. I'd look closely at all the wiring and your solder joints also.
I hope you get it sorted!
R,
Chris