I am dual boot Ubuntu 12.04 64 bit/WinXP. I have been having daily, ongoing startup problems but after a couple of hard shutdowns my computer stabilizes and the rest of the session is uneventful.

I was reading an Ubuntu Documentation on Partitioning/Home/Moving and the last section got my attention
Different filesystems on the same disk
If you're moving from Windows and your new home partition is going to be an old ntfs partition (the D: disk) while you convert the C: disk to a journaling partition where you install Linux, this won't work, there will be a huge load on the processor. You should convert the two partitions to ext3 or ext4 or keep both partitions as ntfs (I haven't checked this last option). But working with two different filesystems on the same drive simultaneously doesn't seem to be a good option.
I currently have both ntfs and ext4 on my hard drive and the same setup on my external drive. My processor is working extra hard the first several minutes of a session as shown by System Monitor. Am I reading this right that my existing hard drive setup is not recommended? Does this mean that the drive should only contain ntfs as long as I have WinXP in dual boot?