I've just runned tklpatch-extract-iso (indirectly from the top level script) and got:

create_inode: socket turnkey-redmine-11.0-lucid-x86.rootfs/var/run/mysqld/mysqld.sock ignored

while extracting the fs. Maybe mysqld was not stopped? I'll keep an eye if this happens again, but just wanted to report this. 

I hope it won't be an issue for my experiment.