Assuming the batteries haven't actually reached the end of their useful life, there's a possibility the internal clock battery is failing, consequently drawing too much power from the main battery.
A test for this would be to leave the camera with the battery removed for maybe an hour, then refit the battery and check if the clock/calendar needs resetting.
I have two bodies with this problem, my K-01 and a Samsung NX5, and I simply leave the camera with no battery fitted until I want to use it, at which point I fit the battery and reset the clock/calendar … takes but a few seconds
This is not a big deal … no other stored camera settings are affected by a flat battery!
A test for the batteries might be to fully charge them, then leave them not in the camera for an extended period of time before fitting them and checking the charge state.
If it's noticeably diminished, the battery is reaching the end of it's usable life.
Do note, in my experience, OEM batteries, both D-Li90 and D-Li109, will both hold a relatively full charge for very many months, whereas third-party batteries will often fail this test, even when relatively new!