All of the data and layouts should appear in the converted copy of your file.
Perhaps your file is damaged in some way that is not obvious in FM 6 but which creates issues during the file conversion.
Try recovering a copy of your FM 6 files and then try converting the recovered copy.
As a last resort, you'll at least be able to import all of your data if you export the data to a tab file of one type or another and then import this file's data into the converted copy.
Here's a useful Knowledge Base article on file conversion: http://help.filemaker.com/app/answers/detail/a_id/750/kw/converting