UPDATE: I can confirm that one application (PlayerPRO) reproduces this every time if it crashes on launch. This is caused by the way it uses OS X's audio system - it tries to restore the state of its mixer, and as part of this process, initializes the mixer (which sets the balance to 100% right). Then, before it sets all the parameters, it crashes, leaving the balance 100% right. Annoying.
That being the case, are any of you using OS X applications that do audio heavy lifting? These include applications that have advanced audio composition (Logic Pro X etc., audio redirection apps (Airfoil etc.), and audio capture (Soundflower and all apps that use it, Audio Hijack, etc.). These apps can sometimes do goofy things with OS X's audio system, especially if they run at startup. Try disabling their startup behavior and see if that helps.