Further clarification: When you have the screen on, it is using the incoming juice to power the iPad as much as it can, so it won't charge at the same time. This doesn't mean that when it's off, it won't charge or it considers the charge negligible; it simply means that it can't charge and use the power at the same time to keep from draining the battery. So while it may not charge while plugged in and on, it will eat up battery life slower than if it were not plugged in. But this won't help much if you're playing games that drain a lot of battery, have the screen turned to max brightness, etc. ;-)
I expect even with a high powered port, it will charge more/better/faster if you're not using it, i.e., not consuming power. "Not charging" simply means, in this case, that you're using more power than is coming in by just having the screen on. People at my office with low powered USB ports thought that it wasn't charging their iPads for the same reason; I have the same computer and left my iPad plugged into my computer and left my iPad off--sure enough, when I checked later in the day, the % battery had risen. (Some are annoyed that it needs so much juice that it can't both charge and power the iPad at the same time from a lower-powered port....)
This is a frequent source of confusion; there's too little space and Apple can't fit all that info into the little part of the top line on the screen. ;-)