It sounds to me like the iPad Mini is charging the way it was designed to charge. I don't think that Apple states anywhere that using an extension cord is a recommended way to charge the device.
Having said that, I have been using extension cords with my iPads since day one with no issues at all. Are you sure that the extension cord isn't bad?
The quickest way to charge your iPad is with the included USB Power Adapter. iPad will also charge, although more slowly, when attached to a computer with a high-power USB port. When attached to a computer via a standard USB port (most PCs or older Mac computers) iPad will charge, but only when it's in sleep mode. Make sure your computer is on while charging iPad via USB. If iPad is connected to a computer that’s turned off or is in sleep or standby mode, the iPad battery will continue to drain.
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I am, like thousand of other Ipad mini fans, that experienced the same problem. The ipad was not charging with the charger it came with. At the mids of my frustration I sent the Ipad to Apple to have it cheked thinking there was something wrong with it. They sent it back to me saying there was nothing wrong with it. The problem persisted. A friend told me to try the more powerful 12 W charger. I did but the improvement was very marginal. Just two points in 48 hours of continuing charge. I was about to return the Ipad to Apple and ask for an exchange or the money back but I decided to try another cable. I bought a USB- male 30 pin adapter connected to a female 30-pin-lighning adapter and it charged to 100% in six hours .I have had no charging problems ever since. The cheap charger that comes with the Ipad is giving Apple a very bad reputation. It is a 5 cents cable that is costling Apple too much.