Has anyone answered this question? I am having the exact same problem.
What I have done as a quick fix is to only render the “Needs Rendering” and “Preview” (the red and neon green render colors, respectively) of the sequence manually (Render Only, under the Sequence menu), turn off the auto render in User Preferences (bottom right in the general tab), so it doesn’t render on it’s own and cancel out the running multiclip in the viewer. The other colors of “needs rendering” types look fine during play back.
When I am pretty much done with my edit, then I render the whole thing.
I would be nice to figure out how to actually solve this problem, if someone out there knows.
Good luck.