My first suggestion would be to work on progressing to flying in idle up mode to keep a constant speed to your rotor. A flat or very shallow throttle curve (100,95,90,95,100) will help make it easier to fly, even though it may be a bit intimidating at first.

As far as the old batteries out running the new ones, you may have gotten some bad batts. I am down to only a few batteries at the moment and I am getting 4.30 min (timer set to 4:30) out of a 2200mah 20c battery running a flat throttle curve of 100 on a 3800kv motor and 12T pinion. My flying is mild 3D. I can gain about a minute to my flight time if I run in normal mode with a throttle curve (40,75,80,80,80).