I don't see how it could possibly be the motherboard. Data from PS/2 and USB keyboards take a completely different path through the system, and the 'd' key sends the exact same keyboard scan code whether the Shift key is being held down or not (the Shift key is actually handled by the OS, not inside the keyboard).
Does the system seem to be stable otherwise?
This sounds like a software issue to me, possibly malware. I could imagine a malfunctioning keylogger occasionally swallowing keystrokes.
Try booting a Linux live CD and see if the problem persists.
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