FileMaker 6 didn't have account names, so when converted, the existing passwords use the password as the account name. Thus, you can open the file by entering the password in both the account name and password boxes. Once you have the file open, you can update these settings by entering your own account names to keep people from reading passwords over your shoulder when you enter them in the account name box.
Passwords in FileMaker 11 are also case sensitive where they were not in FileMaker 6. If you still have FileMaker 6, open the original file and check the passwords to see how they are spelled and how they are capitalized. Then enter exactly what you saw as the password in the converted copy.
For more on File conversion issues see: http://help.filemaker.com/app/answers/detail/a_id/750/kw/converting
Thanks for your answer it worked a treat.