I wanted to help my gf out by installing Puppy Linux on her old computer so she can get on it quickly for the internet and do things when her laptop isn't available.
Her hard drive was already pre-partitioned by the manufacturer and had 4 partitions so i decided to overwrite the backup partition (hda3) and do a full install to there, as she never backed up her files on it and it was empty except for the journaling system.
The install was successful, I also put grub on that partition and changed it's flag to bootable. I re-started the computer and grub came up nicely and i was able to get right into Puppy. But when I re-booted again and tried windows the screen flashed some text (too fast for me to read) and then went black and unresponsive. I hard re-booted to find that it by-passed grub and the screen flashed the text again and went black.
I loaded in the live-CD open up gparted and found that the boot flag had been switched back to the windows ntfs partition (hda2)so it will bypass grub.
So that's my problem. I can't boot into anything but Puppy and if I try i can't boot into anything at all. She is not very good with computers, and being most familiar with windows she doesn't always want to work with puppy, so that's why I'm trying to get windows to work for her again.

A recent live CD would be the most convenient tool to help fix this.
One possible route to get everything working:

1. boot live CD
2. reinstall the GRUB bootloader, but install it to the Linux partition
3. make an image of the bootloader sector using 'dd'; copy this image to the winduhs partition
You can read/write ntfs partitions if you mount the partition using the ntfs-3g driver.
To copy the grub bootloader sector, assuming you installed grub to /dev/hda2:
dd if=/dev/hda2 of=grub.img bs=512 count=1
Be extremely careful - 'dd' is a very useful tool but one tiny mistake and it can completely screw up your HD.
4. make a backup copy of the winduhs boot.ini file, then edit the file to chain to the grub bootloader image; this is typically an entry like:
c:\grub.img=Linux
(Or maybe I got that backwards and it should be: Linux=C:\grub.img - google should be able to help you out)

Have a good look at the boot.ini parameters to see if there's anything else which might need some slight alteration. I have no idea how the XP system attempts to maintain its infestation of a computer system. Perhaps you should use google to help you find some notes on how XP attempts to detect changes to the system and 'recover'.