Hi Syed,
I'm just guessing now:
During export you can choose a unload order (by size, by time analyzer results or by name). Your *.EXT files don't cover the missing tables as you say in your first post. They are created during R3szchk execution and they are used by the "by size" method.
If time is not too expensive in your situation, I would try another method like "by name". But again, I'm just guessing here.
Note that you have to remove all files of your export folder, which were created during the export operation before you try it again.
Good Luck and Regards,
Steve