The circuitry inside the battery has to communicate with the system to report it's status. Non-OEM batteries do not follow that and therefore the charge is not communicated correctly.
Recycling the Li-Ion batteries is not a good idea. these batteries do not have memory, but also do not tolerate well complete discharges. When that happens, they lose a few more cells, effectively reducing the battery's capacity every time. It works on Ni-Cd or Ni-Mh, but not Li-Ion.