Until today I had not heard of Finnix.
https://www.finnix.org/
Do you have Finnix installed or are you just running it as a Live CD?
Are you having to use umount cmd each time you want to un-mount that partition with the .iso images?
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Has anyone here had similar issues or found a boot when the filesystem was "unclean"?
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No, but trying to boot up with a Live CD and copying those files to an external or usb flash drive might be a good idea.
Running fsck will help if the fs needs repair.
https://linux.die.net/man/8/fsck
https://wiki.archlinux.org/index.php/fsck
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