I wouldn't recommend writing to NTFS through Linux. NTFS is really a Microsoft trade secret, so the computer kinda guesses what to do, which is bad. I'm not really sure how it works, just that it's not recommended if you want to keep your files happy and uncorrupted. Since you have XP, unless you are attached to that particular install, I'd just format the whole partition to FAT32 and reinstall, both using the XP install CD. Pretty much any system can write to FAT.
I'm not sure what the cause of your problem is, but in any case writing to NTFS is a bad idea. It might be a mount problem, or a NTFS problem. My experience here is limited, so I dunno. Check if:
a) /etc/fstab lists the partition as NTFS or auto or whatever. Not sure what it should be, but it could be a possible cause. Although that would give an error message.
b) the captive-ntfs site can help you. If they have a forum, ask there.
c) your partition is not corrupted. Windows booted fine, but check anyway. That might or moght not help, no experience here. Scan the disk for errors and everything.
I suppose you have your own reasons for using JFS. If it all works out, PM me. I'm curious about JFS, since it looks like a good filesystem.
Good Luck.