Each USB port is suppose to support up to 0.5A. Some manufacturers try to skimp by multiplexing multiple external USB ports onto one USB slot on the motherboard. Essentially 0.5A ends up being divided among the multiplexed ports. Normally most devices like USB drives and card readers don't draw that much current, so you can use multiple of them simultaneously and not have problems. However with the iPad, it needs at minimum 0.5A. So if you want to charge the iPad, then you'll have to disconnect other devices plugged into these multiplexed ports.
It is also the same reason why external USB hubs without an external AC adapter doesn't charge the iPad either.