More than likely what is happening...
Cells are imbalanced. As you charge, one or more of the cells reaches maximum voltage which is usually 3.65 which turns off all charging. The total pack doesn't get high enough to start balancing because you have one or more very low cells.
If you can't take the pack apart to charge the low cells individually, you might want to discharge down to around 10.5V and then start charging again. This is essence is trying to perform a low balance.
This is why LiFePO4 batteries are not good for usage where batteries tend to sit around a long time not used. It's also why EVs with LiFePO4 want to be charged to 100% all the time...so they can get their cells top balanced regularly.
A friend of mine did exactly what you did...let his LiFePO4 batteries sit along time. I was able to recover one of them for him but the other was beyond recovery. I was able to take apart the battery and charge each cell with a power supply set to 3.5V. You need to set the power supple to 3.5V and then hook up the supply. The voltage will gradually come up to 3.5V.
