I am running a multi site in subdirectories, some subdirectories are mapped to sub domains by domain mapping ,
recently after installing templates or plugins (and activating them!) I do not anything added in my plugin or them list in network admin panel,
the amazing thing is that i can see plugin or template succefully installed via ftp!!
just for info: I have already successfully installed and used many plugins and templates like, wp minify, wp optimize, quick cache and seo ultimate (which is basically a massive error generating plugin), here is my link