Internal Resistance is most likely the culprit. As the packs go through cycles their internal resistance (IR) increases which is an indication of degradation of the battery. A good charger can give you an indication what your baseline is when you get a new battery. You can monitor the IR over time and have and idea of the overall "health" of your battery. Connectors as mentioned above also could be a culprit of short run times.
Keeping the LiPo at a storage charge (around 3.85v/cell) when not using helps to keep the IRs low. Storing the Lipo fully charged degrades the battery over time thus increasing IR. Not discharging the battery more then 80% of its capacity improves longevity. Heat is another enemy of the LiPo whether stored or running hard. Another thing to look at when charging keep an eye on each cell. A cell or two can go bad in a pack, bringing down the "health" of your battery and effect run times. Some chargers, when not using balance charging will overcharge a good cell(s) to satisfy the overall voltage (based on cell count) of the battery by compensating for the bad cell. This is dangerous (think fire) and can also kill battery run-times.
Usually a battery that has been designed for high discharge (low IR) such as a 25c (or above) battery can generally be charged above 1C with a good balance charger that monitors each cell. My 6 cell 5000mAh cells I regularly charge at 20 Amps safely. That's 4C and I have documented 300 cycles with 1miliohm change in IR. These cells are used in my 6000W 12 cell EDF jet.
Please note that the above is based on my experience of LiPo batteries and there are many other factors that can effect performance of batteries.