Comment 103 for bug 952080
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a60fb26
(Get the code!)
I don't think any programs will show any difference as a result of the jumper change. Both lines carry +5 V power; the only difference is that one of the lines gets turned off when the system is suspended (or powered down) and the other doesn't.
You'd probably be able to see a difference if you examine the dmesg log after suspending and resuming the system. But that won't help solve the problem.