I'm having a similar issue with a new installation of 0.9.1.1 - on the admin theme, a number of URLs are being generated to http://myserver/admin/... as opposed to http://myserver/... (these include links to the /shared javascript libraries in the header of the admin pages, as well as to the /archive directory (which means that thumbnails, etc., aren't loading properly in the admin theme).
And, of course, the public site link in the top right does the same thing.
Seems like the creation of URLs is somehow going awry in the admin theme; any ideas on a fix? I remember an issue like this happening maybe a year ana a half ago with one of the proto-Omeka sites (maybe JWA?), but I don't remember what was causing it...