I have just setup a fresh WP 3.5.1 installation inside a "ssl" folder, moved the base site url to the root ("giving WP its own directory") and setup a subdomain multi-site network.
In the wp-admin the "My Sites" menu items for the primary site are working (eg. "[domain]/ssl/wp-admin/post-new.php") however the "Network Admin" menu items are all missing the "/ssl" folder in the links and give a 404 error (eg. "[domain]/wp-admin/network/sites.php")
By manually adding the /ssl in the address bar I can access the network admin pages, however buttons/forms within the network admin pages still seem to leave out the /ssl subfolder.
eg. "Add New" plugin button or "network activating/deactivating" any plugins.
No problems with a root install multisite, only with a subfolder install (which is supposed to work in 3.5?)
Here are the steps I followed:
Help help/advice is appreciated.