When the DGN is of ‘Original File Format’ V7 format, it may be the reason the rotated clipped view is not saving.
Original File Format of a file can be found in:
File>Properties>Statistics> Original File Format
Updating the file to V8 File Format by attaching the file as a reference to a fresh seed, and merging the file into Master, will resolve the issue.
An article on Clipped references and rotated views:
http://communities.bentley.com/communities/other_communities/askinga/w/askinga/clipped-references-and-rotated-views.aspx