[SIZE=+1]Do NOT attempt a restore operation (write to flash) with a Low Battery!!!!![/SIZE]
As your battery gets low, the voltage droops, and it becomes progressively easier with flash devices to get a "weak write" of a page. You are begging for all sorts of nasty things to happen (massive number of pages in your flash marked as bad, corrupted file systems, etc).
I just looked at the nandroid-mobile.sh script, and it checks to see that the battery is at least... wait for it.... wait for it... wait for it.... 30%.
I don't feel comfortable if it's less than 80%, but I am probably overly conservative.
As for the cause of your troubles, it will be apparent in log messages in the /cache/recovery/log file. Amon_RA recovery has a menu option which allows you to copy this file to your SD card for convenience.
Post it up here (the bit with the errors, that section should be obvious) for more feedback.
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