I have a Meike from Adorama. I had no issues until a recent trip to Kenya. When shooting in continuous, it had a habit towards the end of the trip of all of a sudden claiming the battery was dead (both were fully charged). I had to turn the camera off and on when this happened.
I have the MB-D80. But I have the same issue as you. Batteries reported to be dead but at least one of them are fully charged. The issue that was causing this for me was the contacts between the terminals on the camera and the "little fingers" on the grip weren't that great.
If you look at a EN-EL3e battery which you have used for a while on your D90 (directly in body, not with battery grip), compare the "wear" marks on the three terminals / contacts. You will notice the middle one is a bit off (closer to the edge of the battery). With the battery grip, those little fingers sometimes loose contact or have bad contacts with this particular pin. So to solve it, you will have to bend the contact inside the D90 body a little bit.
I did not discover this myself so I can't take credit for this. I did a search on my problem and this seemed to have solve it.