Wow, ok this is a really old post, and you might have already come across the solution, but in case you haven't and anyone else is searching for a solution to this issue, here is the gist:
Maya is dumb.
That's pretty much it. Well, actually yes it is related to plugins, most of the time. The most common issue of this happening is a person has a plugin loaded, (you can test this out as well) and creates a scene file, then either the plugin is unloaded or someone else who tries to load the scene doesn't have the same plugin loaded.
For this example, fire up the maya, and load the Maya Vector Render plugin.
1) Open the render settings window, and set the renderer to the Vector Render, and render a blank frame.
2) Now save the scene as a mayaAscii (.ma).
3) Create a new scene, unload the vector render plugin and close Maya.
NOW! Open Maya back up, make sure the Vector Renderer plugin is unchecked, and try to open that scene up that we just made. You will get an error, but it will load. Now try to save the scene as a Maya binary file.
"ERROR! File contains unknown nodes or data"
Soooo, why is this happening? Well, certain plugins make nodes in your scene. Mental Ray for example, when you load the plugin and open the render settings window, creates a ton of mental ray related nodes that store information for your renders.
Vector Render does the same thing, so when you load the plugin, and render a frame, it creates a "vectorRenderGlobals" node (which is hidden by default), which contains settings for your vector renders.
When you unload the plugin, Maya doesn't know what that node is anymore, and it complains. You will either have to load the plugin up, so Maya knows what it is, or delete the node altogether.
To test this out, repeat the same steps as before, but this time with the outliner open, and turn "Show DAG Objects Only" to "OFF" (right click in the outliner). You'll notice after you render a frame with the vector renderer, the vectorRenderGlobals node appears.
You can also try to delete the vectorRenderGlobals node with the Maya Vector Renderer plugin unloaded, and it will save fine.
Hope this helps! Cheers!