I've been reading this similar thread having a related problem and maybe you can give me any idea to deal with.
In short: a plugin needs to use a text file to work. I use the plugin at subdomain blog with an media uploaded txt file and this is replicated via mu-sitewide-tags plugin to main blog and there file seems not to be accessible to main blog post.
.- I'm using OSM Plugin to use maps on posts. This plugin use txt file to put a second layer on map with gps/kml tracks, thumbnails...
.- This is the subdomain post:
It uses file http://colegota.mapamundi.info/files/2010/12/egon-marcadores.txt uploaded previously to multimedia library.
.- If you see the post from a main blog page like a category page it can't find txt file and can't show track and photos in map. Example:
Before migrate to multisite I have that files under colegota.mapamundi.info/gpx/... or similar folders and replicated post in main blog using syndication, then were no problem. But now, with WP managing * subdomains, subfolders are not accessible.