Is the C: drive IDE or SCSI? The BIOS of some systems allow you to set the boot order of your drives (ie floppy, CDROM, SCSI, hard drive) - the last "hard drive" is the imbedded IDE controller on the motherboard.<br>
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Another thing to try is remove the IDE drive temporarily, boot and install Win 98 to the SCSI drive, then reinstall the IDE drive after the completed install and change the MSDOS.SYS file. MSDOS.SYS is simply a text file now with Win9x and there is an entry for the Windows directory, you should be able to change that to D:\windows -- that may work. I have never done it, but in theory it should work.<br>