The 1-series bodies take only a single battery (but it's a big one). I have not experienced any of the issues you're describing. I have found battery drain to be predictable, the only variable is the type of shooting I am doing. When taking lots of bursts (which happen fast on a 1D X) I get a lot of shots per battery charge, with a relatively slow drain. When doing a lot of live you shooting, drain is faster, but still proceeds at a steady pace.
You might consider contacting Canon service. Possible things to try before that would be to reset all of the camera settings to the factory default using that menu option (if you have a complex set up already, you can write those settings to a card and reload them later if that doesn't help), or a full reset (remove the main battery and the coin-cell clock battery, leave them out for a few minutes, then put them back in).