the sensible thing would be to have the linux hard drive as the slave on the primary channel so both operating systems can communicate at an optimum with the cd-rom. check your drives wouldnt be better with an 80 conductor cable and the jumpers set to cable select.
Not sure quite what you're asking, but you need to connect the master and slave on the right part of the cable. If you get them the wrong way round they won't work. I have my 2 cd-roms on the secondary IDE, and two hdd's on the primary IDE.
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