Thanks for the details! It took me a long time to figure this one out, but I have found the source of the problem. After the search override, some post type links were not filtered in the way I expected, and the permalink was reset to the original link. WordPress unfortunately does not allow displaying items from other than currently active blog from within one loop.
I have implemented a fix directly to the search, by forcing all the result post types to “post”, which then executed the proper override to change the URLs to the correct one. The URLs in the results should be pointing to the correct blog now. Will answer your other tickets as well, as soon as I can.
I will include this fix in the next plugin update, so you don't have to bother with it anymore.Best,
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