Tough to say, but what i know is that the export and import functions in AE are crap, you are better off just opening the files from the project window, that is double clicking on the project window area and looking for it on the menu that pops up, and then dragging it into the composition area. If you do it this way you are telling AE to find out what format and setting the file is and and THEN open it, rather than telling AE what format and settings you want to use and then bringing in a file and playing it, which is what import does.

Is that what you are doing or are you using the import export menu?