Wait a second, I am wrong about the CIR header.
Question first, the single USB header you mentioned in your first post, that was connected to the CIR header, is that plug a four pin USB to mobo connector, or a nine pin USB to mobo connector?
The CIR header is placed next to the USB header, with matching pin spacing, by design, on purpose. In order to use the CIR/remote control feature on this board, a separate remote control receiver must be connected to the PC, via a USB port. That USB port becomes a dedicated connection for the remote control receiver. The cable from that USB port must use a nine pin USB to mobo connector (or two four pin connectors?), with one row of pins on the CIR header, and another row of pins on the USB header. This is explained on page 34 of the manual, with clear pictures. So my bad, too.
Given the pin assignments of the CIR and USB headers, I can't see how connecting a USB to mobo connector to the CIR header would damage anything. The power and ground pins are in the same location, and the other pins are the signal/data pins. Plus, the CIR header +5V pin is powered by the +5V Stand By source of the PS, which is not incompatible with USB power standards, which is +5V.
Bottom line, I don't think anything was damaged connecting it as you did, since the PC ran fine with it that way at first. Did you ever connect anything to that USB header on the case? Or never used it?
Have you tried disabling the CIR feature in the BIOS? It is enabled by default. If you can get into Windows, it would be interesting to see what your original connection to the CIR header was interpreted as by Windows, in Device Manager.
Sorry, this is not really helping much. BTW, what OS are you using?
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