I saw an earlier bug (that has since been fixed) with package servers, that was quite similar. If you did a specific assignment on package servers for a package, and clicked ok
on the same tab\page that you made the change on, despite what the dialogs tell you the changes were not saved.
However, if you went back to the original tab (that opens when you doubleclick on the package) and then click on save changes and ok, the package server assignment was saved.
So, in a long winded way of answering your question, try saving the changes on the first tab of the area you are modifying.