Did you check your running processes using spyware etc?
And, it also depends upon your partitions as i said.
A FAT 32 partition will work slower on win2k than a NTFS partition. It also depends upon the data on your partition.
I think you must be using different partitions for each OS?
The seek times on the HDD are also diff for different locations in your HDD.
*Thread title changed and moved to troubleshooting*