I have a similar problem. But first , some help for you. I have two separate discs one for Linux and one for Windows. I have installed Linux (Red Hat 9.0) on one disc and Win98 (C
and Win2k( D: & E
on the other. I am using GRUB as Boot Loader.
On booting I see the GRUB Menu which gives me a choice of "Linux" or "Windows".
BTW you need to modify the GRUB.conf file (/boot/GRUB/) to get the above options. You will get the necessary info if you visit the GRUB homepage. Also you need to change the boot sequence of your hard disc to ensure that the Linux HDD is your first disc.
On choosing Linux i am able to boot into Linux, when i choose Windows i get the Windows boot loader menu. This is where my trouble starts- if i choose Windows2000 i get the "ntoskrnl.exe missing or corrupt..." error, if i choose Windows 98 my system hangs!!.
Need help in booting windows.