Not sure if this is a limitation of Google Chrome, but if I have several of the plugin folders processed by the Google Chrome launcher, multiple --extra-plugin-dir command line arguments will be generated, and only the last one will take effect.
That means that since Java is the first one processed, it will be the first --extra-plugin-dir and will be ignored by Chrome if Flash, Silverlight, and/or BrowserPlugins folders exist.
Simple test: install jPortable, and also put Silverlight files into the PortableApps/CommonFiles/Silverlight/files folder. Chrome will be launched with 2 --extra-plugin-dir arguments, and only Silverlight will be loaded. Rename the Silverlight folder, relaunch, and Java is back (but no Silverlight, obviously).
Any ideas how to resolve this? I love the idea of one place for plugin files that work with multiple browser versions, or even multiple brands of browsers. Firefox allows for semi-colon separated folder lists in an environment variable, but I couldn't get that to work with Chrome so far.
When I implemented it, I'd tested it and it did work at the time with multiple instances of the command line argument (at least as far as I can recall, I could be mistaken). If it doesn't work now, it's just another limitation of Chrome/Chromium. Perhaps we'll make it selectable for Chrome which plugin you want to use and have it continue working with Firefox, SeaMonkey, Opera, etc which all support multiple plugin directories.
Sometimes, the impossible can become possible, if you're awesome!