I know I just wrote a long e-mail on this, but I think I just figured out in my own mind exactly what is going on and wanted to document it.
As others have said the /etc/apt/trusted.gpg file is the issue. It seems that what is happening is this: 1. For some reason the first use of software-properties-gtk creates this file, but (the bug I presume) is that it's not created correctly. It's empty and potentially has the wrong permissions on it. a. I suspect it being empty is the consequence of the permissions, but I am just guessing. 2. Running 'apt-get update' will now produce errors about user "_apt" and not being able to read the /etc/apt/trusted.gpg file. 3. Making /etc/apt/trusted.gpg readable (i.e., 0600 --> 0644) only obfuscates the problem; now the empty file is accessible (so no errors about reading it), but the keys are not available and /etc/apt/trusted.gpg.d is now ignored and results in key errors. [Wild goose chase may now commence]. 4. The real fix is to delete /etc/apt/trusted.gpg and after that point it seems not to be created again (even if running software-properties-gtk). Everything works again since the /etc/apt/trusted.gpg.d folder can once again be interrogated. Hopefully this post isn't just adding noise, but I thought a short description of the issue in one post could be useful for posterity.
