Today I was flying and was using 3000mAh battery's for lap time of 5.3  then I went to my other battery that is 3300mAh and the flights were 5.0 lap times is 300 mAh that a big change?

Yes Castle control line mode on Pheonix 45 esc and hubin timer on Pheonix high RPM setting.

Yep gov. High. Hub in fm 9 on hi RPM batt. Were charged to 100% with Cell-pro 10 flights only diffrence was Rpm. Not that bad 5.3.  And 5.0. No changes made except batt.  3000aMh to.  3300 aMh

John   I did not tac. the RPM's as it was not a big thing in flying, I was surprise that infact there was a change , just because of diffrent battery

If you can't get an RPM easily, letting us know line length, airplane used (or weight and span), and prop used (diameter, pitch and brand) will kinda sorta not-very-reliably let us know if your RPM was in the ballpark of being able to be regulated.  Stepping out into the driveway and getting a quick RPM reading would be much, much better.

Basically, your regulated RPM needs to be no more than 75% to 80% of your calculated RPM, where your calculated RPM is Kv times the nominal pack voltage (and nominal pack voltage is 3.7V per cell).

I suspect that what's happening is that the smaller battery also has a higher internal resistance; this higher internal resistance means less voltage available to the ESC, which means less voltage to the motor, which means a lower speed.  What's the "C" rating on the packs, and are they the same brand?  "C" ratings are pretty loosey-goosey, but given two packs from a reputable manufacturer with differenc "C" ratings, you could reasonably expect that the one with the higher "C" rating will have a lower internal resistance.

Quick glance is Motor is E-Flght 25  870 kv ,  the battery is Sky Lipo 3300mAh 4cell 20c    Zippy 3000mAh 4cell 20c

I dunno about Sky, but AFAIK Zippy is a pretty cheapo brand -- so you can expect that their "20C" number is toward the "won't burst into flame if used this way" category, rather than "won't significantly shorten the life of the battery" or "will work solidly".

(870 RPM/volt) * (4 cells) * (3.7 V/cell) = 12,900 RPM.  That's the RPM you could expect if you take off the prop and run the thing when the cells are at 3.7V.  Put a prop on and the current draw will reduce that.  Get to the end of a flight and it'll be lower yet.  You need to have your governor speed set above that "high current, end-of-flight" condition.

Using the 75% rule of thumb (I think that's from Dean) you'd need to set it for no more than 9650 RPM at launch.  This is puzzling, because that's a reasonable launch RPM for a 'normal' sized stunter, unless you're using a really flat prop or a really small-diameter steeply pitched prop.

Somehow I suspect that you're just setting your RPM too high, and that you need to reduce the RPM to match your motor and cell count, then juggle prop pitch and reduced RPM to get the lap times right.

Hi Larry,
It's like Tim said, in order for the governor to do its thing, you have to be within range.
For one thing, what RPM did you set in the Hubin timer?
Next, did you pick the right pole-count into the timer and ESC?
lastly, you should be able to run brief ground checks with ... the normal flying prop, a s;lightly smaller one, and a much much smallewr one and prove to yourself, with a tachometer, that the RPM is the same.
It sounds to me like your governor was pinned at 100% throttle/voltage and then different batteries will fly differently. Also, the lap times will change throughout the flight. That shouldn't happen.

take care,
  Dean P.