Okay, I had Compiz running on Xubuntu 14.04 on a previous install but for some reason the fresh install I did last night won't let me get it running. It seems like Compiz can't read any configuration options and it acts as if I just installed every time I open CCSM. Even to the point that it asks if I want to display the warning screen again.
I've installed dconf-editor and gconf-editor. I've gone back and forth with the backend settings option in CCSM and it reloads all my settings when I switch to GSettings backend but once I run "compiz --replace" I get no borders or effects.
If there's any other info I can give to help diagnose just let me know.
Edit: I figured this out. I fixed the issue by editing /etc/compizconfig/config as root and manually changed the backend to gsettings under the general heading. For good measure I also changed the profile to my custom one. Now Compiz starts up and everything works as expected.