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So after reprinting I noticed that the channel throats (see http://imgur.com/nfRzafJ) were becoming clogged due to my retraction setting. I had the retraction for over 4mm and since this is less Slic3r would just go right over it. I used a knife and tweezers to remove the jam and now it works (though could be better as there is still some blockage).

Not sure if this is your problem but give it a shot. You can even cut the one you have right now and see if it is clogged.

Let me know if this helps.