innobackupex on MyISAM dbs only, locking of innodb

So, I have a very large innodb database. I can store that off easily enough without much locking, by simply limiting the backup to the innodb database. No problem here.

So, I then want to run a backup on some large MyISAM databases. Even though I limit the backup to those, it still does a read lock on all databases, including the innodb one, which defeats the whole purpose of using innobackupex. I can’t think of a good way around that, anyone know of one? (Other than using say a LVM backup method for those of course).