I have an installation of Windows XP Professional sitting next to a Linux installation and FreeBSD installation. I am able to boot into Windows XP with Linux as the active partition (I prefer GRUB over FreeBSD's bootloader).
NTLDR is the Windows bootloader that reads from boot.ini. If you are still having issues with NTLDR, I recommend taking a look at your boot.ini settings. You can mount your NTFS partitions under Linux pretty easily. If you need to write to them, you can use the NTFS-3g driver.
You can use:
Where "hda" is your drive. This will show the partition layout.