Don't worry! You aren't alone! I had the same problem as you (I assume) are having (if this post is still valid). If you're putting your energy cells directly on your AE system so that the controller sees them in the system, and the system is powered, then they are charging. You may think they are not as when you break them with anything but a wrench (I use the Thermal Expansion wrench) they lose any stored power. You will know they are charging as they begin to glow in a "filling" pattern much the same way OpenBlocks tanks fill with liquid from bottom to top. Hope this helps sir!
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How do you charge an energy cell (Applied Energistics)