I read on on a forum (can't remember where) that there is a bug regarding led notifications. If you link to a Google account when initially setting up the phone the led notifications don't work, so the advice is to skip linking to a Google account at initial setup screens and then add your Google account from the Settings>Accounts later.
Hope this makes sense, I did exactly this and my notification led has always worked as it should.
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Huawei Ascend P6 (White) - 4.2.2 stock, rooted
HP Touchpad 32gb - Cyanogenmod 10.1
HP Pre3 - webOS 2.2.4