Comment 1 for bug 383337

That is true - I tried to document this in the man page, but probably need to add the relpath option to this as well:

"Note that this functionality currently assumes the default InnoDB configuration - it does not work properly if you use options like --innodb-file-per-table, --innodb-data-home-dir, --innodb-data-file-path or --innodb-log-group-home-dir that modify the default file layout for InnoDB tables."

To fix this we would have to parse the my.cnf file for these options and take them into account. This is currently not implemented, but patches are always welcome :)