The molecular assembler block may not connect channels, since it doesn't need one for itself. It does need power though. My recommendation: use smart cable and check how many channels you're using. With three interfaces you should use three channels, but I suspect you're connecting only one of the interfaces and none of the molecular assemblers. The crafting monitors show the tasks scheduled by your crafting processors, not what's actually been sent to the MAC. Also, give the molecular assembler blocks their own cable connection.
My setup usually looks like this from above (M=Mac, X=interfaces, -+ = cable):
And like this from the side:
Code:
+X+X+
+-+-+
+X+X+
+++++-----
So have a cable going into the bottom of every assembler to give it power, and stack an assembler with five microblock-ed interfaces every two blocks in height. I'll post a screenshot when I get home.