i recently replaced some aging EIDE drives with new ones. Now the operating system insists on making my slave drive the master drive and vice-versa. needless to say it won't boot because the operating system is on the 'slave' drive. no matter how i set the jumpers it insist the drive with the operating system is the slave. the BIOS though, recognizes them correctly. THis is really baffling me.
Did you check to make sure that the EIDE cables that connect to the back of the hard drive, are connected correctly? Because the end one is for the master H.D. and the connection in the middle is for the second H.D. Also, check Microsoft or Western Digital sites. They have the chart for the proper jumper settings. Good Luck.