Hi,
According to section 3.2.1 of the board's TRM (download here), the voltages seem good (I get the similar voltages on my C6678 EVM), therefore the issue must be on the mezzanine card itself.
Given the supply is fine and the mezzanine can't be recognized by Windows, I don't see a way to reflash it (all utilities require that at least the board is enumerated by the USB interface). I feel sorry for the trouble you are having, but unfortunately the symptoms indicate your mezzanine board failed and you can't do much more other than try to repair or return it.
Unfortunately due to the complexity of these boards, issues like these usually happen suddenly - sometimes with or without apparent reason.
Regards,
Rafael