Strange one, the difference may between your application launcher environment settings and the filetype associations, as in when you open Maya you may be going through a "wrapper" that sets the location of the plugins and such and potentially when you are clicking Maya files directly it's loading up a "dry" Maya environment without the plugin locations. Just a thought, hope this helps but as far as I know the header inside a Maya scene file contains a series of "requires" lines which loads up the listed plugins before going through building/loading the scene itself so it shouldn't skip loading any plugins and list the nodes as unknown unless Maya simply can't find the plugins. If that's the case then the solution is as easy as set your filetype association to launch the "wrapper" rather than the installation binary. No idea how to do that in python though but one way to work around this would be to place a scriptNode inside those scenes which explicitly sets the path to those plugins in question and loads them, but that's kind of going the back way about it :)
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