Problem: When working with a subdirectory install of Multisite (probably the same for subdomain but didn't test) if the subsite has domain mapping enabled, uploaded media does not display.
Solution: You cannot have a subdirectory off of root named /files. Mod_Rewrite cannot operate if the physical directory is existing. Delete or Rename the /files folder and everything works great.
If it is possible you should add to the instructions or provide a check when installing the plugin to check for the existence of such folder.