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I'm making changes with ccsm to the unity plugin, mainly to disable a whole ton of useless keyboard shortcuts which just take fullscreen applications out of focus and cause other problems. The changes however, are all being undone every reboot and when I run ccsm again, all the changes are showing as there, but all the shortcuts become re-enabled. I then have to restore each one to default again, and re-disable it, only to have it happen on the next reboot. How do I get it to save the changes and actually, save the changes instead of just showing them saved?

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At this page https://wiki.archlinux.org/index.php/Compiz_Configuration

You will know about this file:
~/.config/compiz-1/compizconfig/Default.ini

Also you will have to opt for the "Flat-file configuration backend" for the below to work.

So, to FORCE your settings you can do this:
First of all: backup your ~/.config/compiz-1/compizconfig/Default.ini Now, simply put ccsm at startup applications, it will ensure applying Default.ini configurations, as otherwise that file may still be ignored.

If that still doesnt work, you can try this also:
Open your ccsm, go in Preferences/Profile/Export, so you can save your preferences.
Now, copy your preferences to ~/.config/compiz-1/compizconfig/.
Still there, backup the Default.ini file.
Now rename your preferences file to Default.ini.

My changes finally persisted after boot!

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