What is your battery capacity and discharge rate or replacement ma and flight time?

1800 ma replacement in 5.33 minutes flying is 338 ma/minute or about 20 amp/hr.  On a 2500 mah pack, that is about 8C, well over ThunderPower suggested 3 -  4C break in rate.  If the battery was a 5000 mah pack, then about 4C.

If you want to know your actual rates, you need your data.  Time flown, and ma used/replaced.  But, you don't really need that.  Unless you have an unusual situation, most planes on 2700 mah packs are using about 1600 ma - 2100 ma in about 5 minutes, in the range of 20 amps/h average, and about 8 - 10C.  That is average for the flight and peaks well above that.  

So, to the point of battery break in, too high.  You will have to make or buy something specific to get in the 3 - 4C range that TP recommends.  Or, a controlled regenerative discharge at the desired rate.  I prefer to keep high discharges out of the charger because of heat.

http://stunthanger.com/smf/gettin-all-amp'ed-up!/battery-discharger/

Another way to see you battery usage in flight is to use an ESC with data logging and look at current in level flight and peaks.  Level slow flight might be in the 15 amp range and the 5 - 6C range on 2700's.  I see that on 6 cells, but see others data of more like 22 - 24 amp level on 5 cells, so significantly higher "C" if 2700's.

If I recall correctly, the discharge rate of the 306b is limited to 80 watts on internal discharge.  Watts are voltage of the pack x amps of discharge, so the discharge is quite limited, unless you mean regenerative discharge.  Yes, as noted, "controlled regenerative discharge at the desired rate" can get you there.  That may be at maximal regenerative rate, or controlled to less, depending on your needs.  You need a battery, not power source for the charger, and follow the regenerative instructions if you have not done it before. It is not as simple discharge to the charger, and you need a lead acid battery partially discharged to receive the regeneration.

Yep, but it is trial and error to find that load, pitch and diameter, for a given motor, battery cell count and size.  Also, the ESC isn't getting great airflow static though the total load is about 1/2 normal.  Static is of course more load than flying to begin with, and you only want about 40 -50% of flying load.  Most fly on 2700's with 5 or 6 cells and use about 1800 - 2100 ma in 5.3 minutes.  Works out to about 20 - 24 amps/hour or 8-10C as a reasonable generalization.

No "list your set up" for this, but you could be the first.

Plug a servo tester into the ESC, connect an ammeter to the battery and run it wherever you want.  No calculator, no trial and error required.

3 minute run for 471 ma is 157 ma/minute or in 60 minutes, 9420 ma/hr.  9420ma divided by battery capacity is the C rate of discharge, 3.77C.  If you use it on a 2700 ma pack, that would be about 3.5C assuming a similar battery usage.

65% of 2700mah is 1755 ma and at 157 ma/minute, 11.17 minutes.

Try a 10 minute run and see what you get.

If you have a cell checker, you can use that on the cell lead and see what happens to cell voltage under load.

Edit: Make that 8 - 9 minutes, see my next post which takes into account incomplete break in charge.

Actually, I'm happy you asked that.  I try to go between about 4.1 and then down to about 30%.  That said, the you don't want to run close to the 11 minutes calculated above as that should take you down from 4.2 fully charged.  Break in is not fully charged and not fully, meaning down to 20%, discharged.  About 90% to about 30% remaining seems reasonable with +/- 5%.  I haven't seen science on those numbers, but to stay away from the extreme ends.  My not seeing a hard number doesn't mean that it doesn't exist.

So, if 4.1 is about 90% and you go to about 30% remaining, 60% out is 60*27 is about 1620 out.  About 10 minutes at 157/minute.  Try 8 - 9 and see what % is remaining, or what voltage remaining depending on charger capability.  You can always add an increment of discharge more, better than oops, to far.

I found a bit of variation on the internal resistance of cells when the batteries came from the factory and was surprised as TP uses "balanced" cells, from what I read.  2 soft cycles and the IRs were quite close.

If I am understanding this correctly, you charged only to 4V/cell which is only about 75 - 80% depending on charts.

http://helifreak.com/showthread.php?t=333661

If you mean that the 1250 was returned to 4V then the discharge of 1250 from a 2700 ma pack is about 43%, you should be down to the 35% remaining range.  That seems reasonable for break in.  3.2v cutoff with only 4C discharge seems like it would be a bit lower than you wish.  That 3.2 would be reached late in flight with a 8 - 10C discharge.  What was the voltage of the discharged pack after a 5 - 10 minute rest?  Look at the charts referenced and you can get an approximation of the remaining capacity using that rested voltage.

Difficult to interpret the amount if you put in 1250 to get to 4.2v.  Perhaps for break in you went back to 4v/cell and have the amount used.  Use the charts in the reference and aim for a reasonable discharged and rested voltage in the 3.8+ rested range.

Brief summary is to charge to 4 - 4.1V/cell, then discharge to about 3.8+ rested voltage (you may well be close), the charge back to the starting voltage and check input.  Once you have figured all of that you can start a new battery at your set break in voltage and use you system for your chosen and checked minutes, recharge to the starting voltage and repeat your desired times, generally 2 or 3 and you should be good.  I hope that makes some sense :)

Isn't 3.2v much too low to take a lipo cell?
Maybe I don't know what I am taking about, but that seems really low to me.

Datalogs on 5 and 6 cell packs that I've seen show a cell voltage about 3.5 - 3.6V under flying load near the end of flight.  Hopefully you don't get close to 3.2v low volt cutoff with load, and not near with break in load. That default is easily adjusted up or down in 0.1V/cell increments as I recall.