I am glad that you have managed to resolve the issue on your own.
I have just thought of an alternative solution to your problem. In addition to setting the StripAbsoluteAnchorPaths to true, try setting the AnchorPathToStrip as well:
This way you can manually select which paths to strip and the editor will not be confused by ports, sub-sites, etc.
For more information about anchor stripping in the editor, visit the following KB article - http://www.telerik.com/support/kb/article/b454K-kbh-b454T-bme-b454c-bme.aspx
the Telerik team