I believe that the kindle only seems to trickle charge. Not like cellphones that go for a fast charge cycle. So if it's only on your pc briefly it doesn't gain that much charge.
The other reason you may have less charging connected to a pc is if the pc isn't getting enough power to it's usb ports, this usually is only a problem on some laptop/netbooks or if it's connected to an unpowered usb hub.
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