How do I separate ringtone and system volume on JB? I understand that the Ringtone and Notifications have been linked since (probably about) ICS, but I seem to have managed to link the System sound settings to the Ringtone/Notification volume levels on my Nexus 4.

I recently installed a few volume control apps, and I suspect one of them is to blame. I'm almost certain that this didn't used to be the case. I've since removed the suspicious apps, but the volume levels are still linked (I'm using AudioManager to verify the different volume levels).

Are Ringtone and System volumes usually separate? How do I unlink these settings?
In Settings -> Volumes you will want to uncheck Link ringtone &amp; notification volumes

Actual system volume can't be "tied" to ringtone/notification. If this is not what you mean, please edit your question and explain more if possible.