[ubuntu netbook remix] Battery issue

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http://ubuntuforums.org – I've been having a battery issue of sorts, and this seemed like the best place to ask for help. About 2 months ago, I bought a 12000 mAh high capacity battery for my EeePC from an Amazon vendor. At first it seemed like it was having issues with shutting off with a good charge left (like 40%), but then the problem seemed to go away. Then a couple of weeks ago, the computer died (well, XP imploded) and Ubuntu was installed. Now, the battery meter lists the capacity of the battery at 7.3% what it is supposed to be, and the battery life is, if anything, slightly less than the stock 4400 mAh battery. Is there someway I can get Ubuntu to charge it differently, or is it a battery problem? (Hardware)