My personal settings on OS X disappear after booting Windows (XP or 7) on my MacBook Pro
Try to backup and delete the file under ~/Library/Preferences/com.apple.loginitems.plist

This will remove the login item you have and Mac OS X will create a new (clean) one.

For more information:  


Do you by any chance use some kind of app cleaner on your Mac that would delete .plist files?
When on Windows, do you mount your Mac partition with read access?