what is the make/model of your motherboard?
(Regarding the 2 pin vs 3 pin pwr led discrepancy, others have encountered it as well, where the case wires are designed for a 3 pin, but mb uses only 2....)
Some have suggested splitting the cases header connector in two and superglueing the remaining insulated pieces together at the proper distance, or, cut both wires and use a new 2 pin header to match pin layout required by your mainboard...
If your mb requires a 2 pin connector, but case has 3 pins, where the middle is unused, this might be problematic, unless you can relocate the two pins to being beside each other if thats what's required by your mb,,,
A quick few seconds with a soldering iron, and you can fabricate two insulated but separate female pins aswell...
you can substitute the IDE/SATA activity LED and power led (if on similar 2 pin headers) during your troubleshooting, as either will work in either location if the pinout is the same...