WinXP dual boot problem

[yanon]

I have two physical hard drives on my computer. Each hard drive has two partitions. The hard drive on the primary IDE channel has partition e: and f:. The hard drive on the secondary IDE channel has c: and d:. I installed operating systems in the following order: 1)win98se on c:, 2)win2k server on d:, 3)Win XP on e:. Then I removed win2k server according to the instruction on buja.com.

I changed the boot.ini as follow:
original boot.ini

[boot loader]
timeout=3
default=multi(0)disk(0)rdisk(1)partition(1)\WINDOWS
[operating systems]
multi(0)disk(0)rdisk(1)partition(1)\WINDOWS="Microsoft Windows XP Professional" /fastdetect
multi(0)disk(0)rdisk(0)partition(2)\WINNT="Microsoft Windows 2000 Advanced Server" /fastdetect
C:\="Microsoft Windows"

new boot.ini

[boot loader]
timeout=3
default=multi(0)disk(0)rdisk(1)partition(1)\WINDOWS
[operating systems]
multi(0)disk(0)rdisk(1)partition(1)\WINDOWS="Microsoft Windows XP Professional" /fastdetect
C:\="Microsoft Windows"

Then I formatted the d: partition and deleted pagefile.sys from c:. I didn't type "sys c:" and kept the ntdetect.com, ntldr, and bootsect.dos because I still need them to do dual boot between Winxp and Win98 SE.
After rebooting my computer, WinXP loaded correctly; but my system just restarts whenever I tried to shutdown WinXp. I had to boot into Win98SE if I want shutdown my computer. I could think of two methods to fix this problem. One is to do a clean install of WinXp. The other is to do a system restore on Winxp. The latter method will add the Win2K server option back into the boot menu even though Win2K server longer exists on my system. I really don't want to do something that drastic unless I have to. Do you know any other ways to fix this problem?