Hello Ziemas,
By now you should have gained an appreciation of why battery manufacturers utilize the "standard charge" and "standard discharge" to determine the capacity of their batteries. It gives the highest capacities.
Battery capacity is influenced by a number of things, including charge rate, discharge rate, and the amount of time resting between charging and discharging. Consumer cells are rated by the manufacturer according to the results obtained from the standard charge and standard discharge. This is charging at 0.1C for 16 hours, resting for 1 - 4 hours, and then discharging at a 0.2C rate. All of this is done at standard laboratory temperatures and humidity. In some special applications (power tool and RC use), a manufacturer may give the performance based on a 1C charge and a 1C discharge, but that is more the exception than the rule.
To understand why slower charging rates give you more capacity (in general), you will have to do some studying on the electroplating process. Look up the effect of current on plating and you should begin to understand what is going on inside your battery.
Understand, that the standards for testing and determining capacity apply to the battery manufacturers. They do not apply to companies that simply re-label batteries with their own brand name. The companies that re-label are free to put whatever capacity they think will sell on their label. We hope that they would not "hedge" the actual numbers too much, but sometimes they do. That is where independent battery testing comes in...
When using the C9000, your capacities from the Break-In cycle should come very close to matching the labeled capacity on the cell, if the labeled capacity is from the manufacturer and not the marketing department. Charging, and/or discharging at higher rates will result in lower capacities.
However, keep in mind that charging at higher rates has some advantages. You may loose a little capacity, but you will hold voltage a little higher and get better performance from your cells if you charge at higher rates. You will also generate a strong end of charge termination signal that will protect the cell against overcharge damage. Finally, charging at higher rates takes less time, and having a strong end of charge signal means that it is easy to charge partially discharged cells. You end up getting more cycle life because you don't have to completely discharge prior to every charge.
You have discovered that, for your cells, charging and discharging at higher rates yields around 10% less capacity. My cells come in with roughly a 3 – 6% loss. Some cells are different than others.
There are a lot of variables involved in charging. Various chargers may perform differently than the C9000. BrianChan commented that his RC charger charges to a higher state of charge. The main difference is that the RC chargers have a much higher, or no, peak voltage termination. My Schulze can charge to over 2 volts per cell under certain conditions. The original C9000 charged to nearly the same capacities as my Schulze, but people used the C9000 as a consumer charger, rather than a RC charger, and ran into a multitude of missed terminations. The improved C9000 throttled back on "charge completeness" in favor of eliminating all missed terminations.
Ok, I believe that should take care of your first question… for the second one "how can I get a complete charge?" this depends on how you define "complete."
The easiest way is to put the cells in the C9000, dial in a charge rate in the 0.5 – 1.0C range and remove the cells 2 hours after Done appears.
However, if your definition of "complete" is getting the maximum capacity under a 5 hour discharge, then you will have to run a discharge cycle to first empty your cells, then run a Break-In cycle to charge them. Set yourself a timer for 16 hours, and remove the cells prior to the discharge portion of the Break-In cycle begins.
Tom