Hello again ttandc!
First, I'm happy you found the solution to your first problem, that must have been a huge relief. That's the first time I've heard of a corrupted USB stick. But, good to know in case something similar comes up again.
Now, for your problem of missing geometry, there is one test that you can do immediately that will eliminate the FBX plug-in as the source of the problem. Can you please export your file from Max and then re-import it into a clean Max scene. If everything is as it should be, we can say that the plug-in is receiving and storing all your file information correctly.
Secondly, assuming that the plug-in is working, import your FBX file into Maya and open the Outliner. There is a possibility that your geometry is not visible in the viewport because it is hidden due to the visibility on your root node being at off. So, first check to see if the geometry has actually been brought into Maya by confirming that you can see the meshes in the Outliner. If they are there, the next step would be to see if your root node, or any parent node has it's visibility set to off since this is transferred to the children.
This visibility issue has been addressed in the later versions of the plug-in. If you don't have it, you can download version 2012.2 here:
http://usa.autodesk.com/adsk/servlet/pc/item?siteID=123112&id=10775855Let us know what your results are.
Regards,
Carlos.