I think I encountered the same problem while working on a Drupal 7 patch.  First time the patch was run, MySQL started and ran okay, but every attempt thereafter it fails at the beginning where MySQL is started.  I ran tklpatch-extract-iso and tklpatch-chroot without running any of my patch scripts but found the same behavior.

I think it has something to do with `local diversion of /sbin/initctl to /sbin/initctl.distrib'.  Each time it failed, my conf script had exited with an error and exited the chroot leaving MySQL running.  If I deleted the .cdroot and .rootfs files and started over, then following attempts will fail at starting MySQL.  However, if I use tklpatch-chroot to enter the chroot shell and then 'stop mysql'.  I can then exit the chroot and delete the files without needing to reboot.  I hope this is enough of a clue to find and fix the problem.  Perhaps just stopping MySQL before exiting the chroot would be sufficient.