One thought:
The console is currently set to the max clock speed, while this means it drains more power, it also means it needs a higher voltage from the batteries to remain powered up.
Most electronic devices are notorious for turning off when batteries have loads of power left in them (just put 'empty' AAAs from a stereo into a remote for an easy example) because it supplies a voltage which the device thinks it too low (even if it's still capable of powering the device) and turns itself off to ensure it still had enough power to do the shutdown mechanism or it doesn't damage itself by running the device with insufficient power.
With rechargables the voltage lowers faster when it drains (and they have a lower voltage to begin with) which is why devices which take standard AA's etc. almost never get the battery life indicator right when using rechargables