Just spent a couple of hours troubleshooting this problem. I must say it is disappointing to find out that Adobe has known about this bug for about half a year. Does not exactly install confidence in that it is meant as a professional tool.
Right clicking and changing the Source Audio channels fixes the problem, but is a cumbersome solution once we are talking about dozens of clips. (Edit: it is possible to change the Audio Channels on multiple clips at once.)
As a follow up question - is there a tool that can conform/check/correct the project xml files that Premiere generates?