Get a battery analyzer software. Here is a review of 5 different ones: http://www.makeuseof.com/tag/5-tools-analyze-laptop-battery-life/
Check what the analyzer software says about your total capacity, current capacity, etc., and compare this to what Windows is reporting? If Windows is reporting 0% and the analyzer software is reporting 50%, then you know the problem lies with the Windows driver, and you can rely on the analyzer software to indicate true battery life. However, if Windows and the analyzer are in agreement, then @thethirdtwin is correct, and the circuit board of the battery doesn't know how to report the power of the new cells. That will take troubleshooting the battery circuit itself and any firmware on it.