Well, compared to the original charging adapter, the USB port provides only 500 mA current (at maximum); if there's a passive USB hub in between, it's even less. So, depending on the built-in battery of your kindle, you need more than 2 hours per 1000 mAh charging time (if you have a 3.6V LiIon Battery or similar).
The MTP thing .. how does the Kindle show up in yor Device Manager? If it's an unknown device or marked as "?", you miss the correct drivers. Without proper drivers, no data link can be established.
This might also result in slower charging. If the Kindle doesn't recognize the "attached" PC properly (because the PC doesn't communicate with the Kindle) it might switch to a safe charging mode. That's only speculative, but I can't think of another reason
So, get the drivers fixed, MTP should and charging may work better then.