Two comments:
1) Eyes perceive light in a non-linear way, so you must expect that a 50% ON, 50% off cycle do not lead to an exact half-light perception.
2) If your refreshing rate is fast enough, you can send the right levels to the leds, then all off for a lapse of time, the rigt levels again and so on. You can also apply this methhod in a selective way so that the dimmer affects only to some leds.

Regards,
Alfredo del Rio.