I dunno if this is true, it's just jumped into my head, but I'm sure I have a vague memory...
Have you tried turning the onboard sound back on in the BIOS, but then select the other card as the one to use in windows? I used to experience wierd problems like this back in the days of the pentium 1&2, it's the sortof thing I'd try, even though it makes no sense!
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2006 Mac Pro
Dual, dual core xeons @ 2.0Ghz each
2Gb Ram (I'm too poor)
NVidia Geforce 7300Gt 256mb
Onboard Sound - optical out to Logitech Z5500
Digidesign MBox2 output to PMCs
250Gb Drive running both Mac OSX and Windows on seperate partitions, 400Gb Seagate Drive for Windows, 400Gb WD Drive for OSX
24¨ Acer AL2416W (not nearly as bad as you'd think)
Various Lacie external drives
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