I think what you're running into is related to SE's new ability to scan for all users with a single installation, rather than requiring a separate installation for each one.
One of the features of SE is that it now restricts the ability of non-admin users to "play" with a number of settings, such as the ignore list, so that they stay as originally set by the admin. Why the skin(s) is/are included in this security feature, I frankly haven't got a clue.