Hello,
I'm not sure on what the issue is, but maybe these forum threads may solve your needs:
http://forums.ni.com/ni/board/message?board.id=170&message.id=67378&requireLogin=False
http://forums.ni.com/ni/board/message?board.id=170&message.id=13178&requireLogin=False
Another idea would be to simply not use the file popup but a path control, tree control, etc...(or finally use a Win32 API function call for this, but you would need to use another programming language to create the DLL).
Regards,
Jorge M.