That's very, very weird. Did the mods come via Steam or manually downloaded? If the latter, does the user that the Civ5 executable is running as have read permission on the .civ5mod files?
If you manually extract one or two of the .civ5mod files, do the mods show up in the Mod Browser screen?
If you subscribe to a mod via Steam, does it work, and if so, does the mod sub-directory show up in the MODS sub-dir that the .civ5mod files are located in? (Both Win7 and Win8 do weird virtualization of the directory structure, so sometimes what you're looking at isn't actually where you think it is!)