Welcome to the Forums, Mumbles!
The problem is, Windows stores file ownership and permissions information in a specific way. Users are identified not by their usernames, but by certain alpha-numeric strings. The registry contains information that relates these strings to actual usernames.
Now, if you try to access a hard drive created in one Windows OS by another - say in a dual-boot scenario, then the second Windows will have no way to translate those user-identifier strings into names, so you will see these strings in explorer if you choose the details view with the owner column present. If you have restricted access to some files and folders by manually editing permissions, then it's possible that access will be denied by the second Windows and the only possibility to access the files would be by taking ownership, which you can do by logging in as an administrator.
Similarly, Ubuntu will be able to edit NTFS permissions. The permissions themselves are not part of the registry, so whatever Ubuntu does will stay with the files. But by taking ownership in Ubuntu, you will deny yourself future access in Windows.
The only way that I know of - and I would be happy to learn a better way - making access possible from all OS on your computer or network is to make the files in question accessible by Everyone. if, however, you really want to restrict access, but then want to be able to open the files in another OS, then you could manually edit permissions using those string identifiers, but this is quite tedious and not worth the effort in most circumstances.
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