Trogl :
I have ubuntu on a 120gb external HDD, small 7 gb partition for linux and the rest is NTFS. After I connect it to a windows computer, linux won't boot up and I have to reinstall it.
A little bit more information as to what exactly you're seeing when attempting to boot the drive (after you've used it on a Windows machine) would be helpful, as well as the type of use when it's hooked up to the Windows machine.
Simply plugging it into a Windows machine and reading/writing to the NTFS partition should cause any issues, but Windows doesn't like when removable storage devices with a filesystem it doesn't know how to access can prompt it to ask you to reformat it, which obviously is a bad idea.
Get back to us with a little more info, please.