Caveat, I don't have this charger, most of this type have similar or exactly the same programming though
Mine has similar features.
There is a timer on the charger that stops the charger after 2 hours, this is set to "on" as default as a safety feature when charging Li-Po, however when charging Lead batteries or some Ni-Mh at low charge rates it is easy to be not fully charged when the timer stops the charging process.
Mine also has a max mAH stop as well which was set at 5000 mAH, again a safety feature for Li-po (mine is a pain to set for individual batteries
) so I disabled that as well.
Does your unit display the mAH and voltage at the end of the charge as well?