Could be one of a couple of things.
Your throttle curve should be pretty much at max around mid stick, otherwise your ESC isn't running at optimum efficiency. If your throttle curve isn't runnign between 90% - 100% it will be simply dissapating the unused voltage/current as heat.
But the clue is in how much you're putting back into your pack. Either your ESC BEC is cutting in way too soon - but since you don't mention what speed controller you have I can't say - or, your batteries are buckling under way sooner than they should.
If you've only got the single pack you might want to get a spare in any case, and make sure you get a pack of a known quantity which people are using on these helis. Either a Thunderpower or Flightpower product is a good starting point. You could do with a couple of batteries anyway, and this should help to eleminate the source of the problem. If both batteries behave the same then I'd look at the speed controller.