Yes, probably just the battery dying...
The batteries on Zauri sometimes drop rather rapidly after getting to a certain point. Also, unless this differs on the C-series, the battery meter is not incredibly accurate (showing 100, 75, 50, 25, 10 and 5 %s only), possibly meaning you had less battery than you thought.
And as far as I know the time is stored whenever the Zaurus is shutdown, improperly or otherwise, in the newer models (non-5000/5500).