Assuming what you consider very warm really is abnormally warm (heating is normal to a degree, you can find records of the internal optical/battery/sensor temperature sensors during timelapses on the forum for some cameras) and that your batteries are (or were) good, my best guess is that your camera is broken and consumes a huge amount of current, enough to heat up the battery and whatever faulty part that is discharging it.
You can try to verify by removing CHDK and playing around with the camera powered on in a similar fashion using the same batteries recharged.
