Lithium-ion battery packs, like most other secondary (i.e., rechargeable) batteries, very typically "recover" to a slightly higher voltage level when allowed to rest for a short period after use. This characteristic is different from primary (non-rechargeable) batteries like standard AA alkaline cells - again explaining why the meter reading may change for the same battery after it's been sat in a warm pocket for a while. Apparently, as little as 0.01 of a volt can make the difference between reading full and half-full (or half-empty, depending on your point of view
).
When two BP-511 battery packs are installed in the BG-ED3, the camera draws from the pack with the higher voltage level first until it equals the level of the other battery pack, then both packs are drained simultaneously.
In a recent post, Chuck has confirmed that there is no difference in battery drain whether the camera is off or on provided neither of the LCDs is active. Once the metering display has turned itself off after the requisite six seconds, you can just rely on the shutter button to wake the 10D up rather than turn the camera off and be forced to endure the several seconds' boot-up procedure.
BatteryUniversity has more information about the care and use of batteries of all types including lithium-ion: How to prolong lithium-based batteries.