Yeah i had this happen, and i was a little puzzled...until...
When the iPod is playing mp3s just playing, there is almost no drain on the battery, because it takes almost no power...
Its my assumption that the battery detector is a little inaccurate when it gets down in charge, so if the hard drive spins down, the ipod only is playing mp3s and the detector says you have 2 bars left because thats all that the ipod is currently using...but...when the HD spins up again, this is a HUGE power drain by comparison, similarly, if you have low power turn the backlight on and then wait for it to go off, the battery life meter will increase when the light turns back off, because the amount of power being used decreases dramatically.
Dave