Recovering InnoDB after low disk space problems

Hi,

I use MySQL 5 with a mix of InnoDB and MyISAM tables, and I recently
ran low on disk space due to rapidly expanding log files.

This ultimately caused the mysqld process to stop working (Windows XP),
and it could not be restarted. After copying all of the data files and
re-installing MySQL, I copied the ibdata and two log files across to
the new install, which recovered most of the data. Unfortunately
several (perhaps 40%) of the InnoDB tables were not recovered.

I would hope that there is some way of retreiving these missing tables,
and that they are (for whatever reason) just hidden or not-accessed
within the data files.

Any pointers or suggestions on recovering more of the data would be
gratefully received.