When I replaced my third party grip because it was malfunctioning (draining fully charged batteries overnight with everything off, including AF and IS on the lens), the first two times the batteries were used, they discharged one at a time. After that, they both discharged at the same time. It sort of bugged me so I emailed Canon tech service and the reply that came back suggested both batteries are supposed to discharge at the same time as they are used.
I have no idea why the first two times this wasn't the case. I have two sets of batteries so this did happen with the first use of each set.
Kim (the male variety) Canon 1DX2 | 1D IV | 16-35 f/4 IS | 24-105 f/4 IS | 100L IS macro | 70-200mm f/2.8L IS II | 100-400Lii | 50 f/1.8 STM | Canon 1.4X III
RRS tripod and monopod | 580EXII | Cinch 1 & Loop 3 Special Edition | Editing Encouraged