the software, does it "recognize" the card as the version with SP/DIF, does it show the SP/DIF settings
Yamaha Driver Control Panel Always provides the S/PDIF settings, no matter if it's soldered or not on the board - there is no check - the attached svreenshot is from unmodified card.
Also, if there was a check and S/PDIF is disabled for particular boards in the driver, then we just use approach like "InpOut32" to directly "speak" to the chip and enabled it - similarly how OPL3 is enabled for CMI8738:
I've got the OPL3 synth from a CMI8738 working in Windows 7 x64
check the "tools" folder in "cmiopl.zip" and YMG744 datasheet is publicly available to see the exact settings. So, software is not a problem in every possible case.
To be honest the only and biggest issue with Cobra is what I mentioned in "P.S. #2", because I bet those "hiccups" will probably be present in the S/PDIF too, because it seems they are due to the power supply circuit of the board. Of course, most people won't have powerful electric heater to cause main power fluctuate and trigger the problem. I am also surprised that using different ATX power unit doesn't help at all. So, maybe it's the combination of Cobra power supply circuit and power supply circuit of the PCI slots on my motherboard. However, the fact is - I cannot find any other sound card that has such issue and believe me - I've tried many, including another Cobra card, which means Cobra is at fault. In any way, I hope to find a solution, because I think some capacitor in the power supply of the card is just underrated and they needed to use a better one.