It's pretty clear you don't actually understand how this stuff works, at least on an electrical level. Let me try to clarify.
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but they do not provide all the same amount of current. A typical port will send 1000 mA, but many laptops, in order to drain less battery juice, has less current than that.
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A USB port isn't draining the battery in any way unless its under load (something is plugged into it). Even then, the device only draws the amount of juice it requires, UP TO A CERTAIN MAXIMUM, that is defined in the USB specifications. What you say about laptop manufacturers limiting the maximum current below the USB standard is just not true (provide a source if you want to prove it to me).
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And it happens that when you buy a custom case with some motherboards, there is not the same amount of current going to the front ports as there are at the rear of the computer.
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Again, this is simply not true. If your front ports are not able to provide the maximum current they are suppose to (USB specs), they are not working the way they should.
I've only ever seen something like this happen when someone was using a meager 250W power supply in a system that needed much more (400W+). So the whole system was just underpowered, and as a happenstance, the front USB connectors on most motherboards are pretty far down on the power line. This means that when components are fighting for juice, those connections are going to get shafted.
In any case, if your USB ports can't provide the standard maximum of 1000mA (assuming this is the correct number), something is wrong. It's never the case that they were made to use less juice.