Okay, so the installation looks pretty much like I guessed -- except that you did not use any third party partition management software. That's good for me because it reduces the number of possible candidates for troublemaker, and I just don't have that much experience with them that type of stuff -- especially when used with Win2K or WinXP.
Is there anything else about this system that might be unusual? I've seen both Exchange Server and Active Directory cause behavior of this general type when an unsupported library has sneaked into the mix (usually because WFP has been defeated for some purpose). But, of course, that's looking past the obvious possibility that WinXP might not like being first in the partition order. If so, it wouldn't be the first MS OS to "feel" that way. AFAIK, Microsoft always recommends installing the earlier Windows versions on earlier partitions. I don't seem to recall the knowledge base being specific as to why, though I suspect it has something to do with the handling of boot-time chores and drive geometry issues. Could you post the contents of your boot.ini file? Also, did you try using the "chkdsk /f /r" command on drive d:. (Wouldn't hurt to run it on drive c: either, since you were getting sporadic running on both drives / partitions if I read your message correctly.)
I'm tempted to suggest running "fixboot /mbr" from the WinXP repair console (while booted from the CD), but I'm a little leary of that just because of the unusual configuration. Nonethless, it really shouldn't cause a problem because WinXP most certainly should have rewritten the MBR during installation anyway. In retrosepct, if I had to do what you were doing, I would have placed a small primary NTFS partition on the Maxtor drive, then let the rest of the drive contain the actual WinXP installation. In that way, the loader files would have been in C:, the Win2K installation would have been in D: on the second drive, and the WinXP installation would have been in drive E:. I suspect that might have worked better, though I have to admit that I have no hard data to back me up on that.
My alleged mind is sticking on the idea of this problem having something to do with the differences in the NTFS file systems of the two OSes. I find it interesting, for instance, that you had to "reconstruct" the boot.ini file at all. I would have though that Windows XP's setup procedure would have detected the Windows 2000 installation and included proper reference to it in the boot.ini file, though maybe it doesn't do this so well when the Win2K partition is on a "later" partition. Do you recall the contents of the boot.ini file as it existed immediately after the WinXP installation?
One other thing that might contain a clue -- did you check the system and application logs in the Event Viewer? I wonder if there might be a relevant error message or two in there?
I have to admit that this one has me flummoxed, which isn't really that hard to do.

Since I usually do my system configurations pretty much by the book, working with unusual (in this sense) system configurations is something I'm not used to doing. I've done a lot of testing to destruction of both operating systems in the interests of being reasonably knowledgable about system recovery techniques, but I start with rather plain installations.
I hope something will shake loose. I'll stay tuned in the forlorn hope that I might be helpful. I should have a chance to do a little research on this later today.
- Collin