I have recently installed Ubuntu 4.1 (a distribution based largely on debian) on my Windows system. Now windows doesn't boot.

I have GRUB as the default bootloader. I also used to have both Windows 98 and XP installed.

I only have one hard drive, which had four partitions: one primary (Windows 98) and three other logical drives (within an extended partition), the first of which Windows XP was installed in. So,

C: Win98 (hd0, 0)
D: WinXP (hd0, 4)
E: (hd0, 5)
F: (hd0, 6)

When I installed linux, I resized F to linux swap size, and consequently made E bigger. I installed Linux to E, and made F the swap partition.
When installing GRUB, it recognized Windows and said it's okay to install GRUB to the Master Boot Record. I did as it said, and now Windows doesn't work.

I researched on the Internet, and basically came up with the fact that my having two Windows' installed may be the problem.

Is there any way to fix this without reinstalling Windows and maintaining Linux?

You will have to edit /boot/grub/menu.lst and check what has been configured but you should have lines like this;

title Windows 98
root (hd0,0)
makeactive
chainloader +1

title Windows XP
root (hd0,4)
makeactive
chainloader +1

Once you made these changes then you need to write them to the mbr by doing as root grub-update.

Thanks for the help!