Ok, to my knowledge, there is no way that an existing program (aside from a virus) could both modify a file and remove its' attributes, like boot.ini without direct tampering.
Saying that, your recovery CD simply recreated a boot.ini file from what it had to work with.
This is a standard boot.ini file contents to show you what I mean;
[boot loader]
timeout=30
default=multi(0)disk(0)rdisk(0)partition(1)\WINDOWS
[operating systems]
multi(0)disk(0)rdisk(0)partition(1)\WINDOWS="Microsoft Windows XP Professional" /fastdetect
As far as your start menu being shifted. That has nothing to do with your boot.ini file. Again it leaves me to think someone or some program has damaged the registry and hence this is why you have the start menu issues. Do you have something like stylesxp, deskmod, or windblinds running? Or had any of those running at some point?
If you can, I would really like to see a screen shot of the start menu to get an idea of how things look... I am not sure if you know how to grab a screen shot, so simply press the print screen button on your keep board when the start menu (and programs menu) are up and expanded.
Dani, would probably appreciate it if you crop the picture, to make is smaller and focus on the start menu only.
Good luck!