The message appears regardless of whether the course has content or not, regardless of theme, course layout, or any other settings.
The import completes successfully, however the message appears if any course import is initiated.
The issue reported to us by clients, and tested by us is that the message appears for no apparent reason and is causing confusion EVEN THOUGH the import completes successfully.

Steps to reproduce:

1. Log on to Moodle 2 site as admin
2. SET UP SOURCE COURSE: Site Administration > Courses > Add/Edit Courses > Add a new course > fill in name course id etc. + save. (Nothing to do with IMS whatsoever)
3. Select and enter any course
4. From the Course Administration block, select 'Import'
5. The first import screen appears with a message in red block letters on top of the screen: Your settings have been altered due to unmet dependencies
6. Continue with the import and it will complete successfully