I managed to fix this by changing my package settings. I made my osx downloader preference curl, and it works. My preferences are below:
{
"bootstrapped": true,
"debug": true,
"installed_packages":
[
"Package Control"
],
"downloader_precedence":
{
"linux": [ "curl", "urllib", "wget" ],
"osx": [ "curl", "urllib" ],
"windows": [ "wininet" ]
},
}
I'm in the process of debugging the python. It looks like it's an error with the way the new urllib is behaving with regards to SSL/HTTPS.
If I had to guess I'd say that it was a problem with the script not running as root, and perhaps not being able to read from the CA file, or write the new ones to it.