So, if the inputs to the Thaumatorium read 0, then the suction isn't making it out. If these are directional tubes, perhaps they are oriented incorrectly.
I don't have a setup in my current play through, but I'll check to see if I have a setup in my creative world and post some pictures that may help you out.
EDIT - Here are some images from a system in my test world:
Here are the Furnaces and the Centrifuge connected to the "head" of the buffer chain. You can also see the loopback line comming from the "tail" of the chain and into the bottom of the Centrifuge.
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Here are the buffers that connect the Furnaces and Centrifuge to the rest of the system. Note the orientation of red band on the buffers.
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These are the Jars, 2 per aspect. Note that the Primals are all one normal jar and one void jar. All others are normal warded jars. You can also see how the buffers are configured, and the Thaumatorium and recycle lines at the top.
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Here is the "tail" of the system, showing the loopback line that heads to the Centrifuge, note that there is a buffer with a bellows on it halfway down the line to ensure there is sufficient suction. The red band on that buffer is opposite the others, I.E. it is pointed toward the Centrifuge.
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Here is a view of the Thaumatorium and recycle lines from above. The "head" of the system is on the right, the "tail" (and the Thaumatorium) is on the left. Note how the recycle line (center) connects back into the buffer chain through the buffer at the beginning. The bellows on that buffer provide the suction required on the recycle line to clear the Thaumatorium lines (outside lines) . The recycle line is configured to allow suction from the right, and the Thaumatorium lines suction from the left.
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Here are the pipes leading into the Thaumatorium.
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And a closeup of the Thaumatorium connection itself.
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While the piping into the Thaumatorium looks crazy, it is necessary. Each tube leading from the jars to the Thaumatorium (the outside lines) also needs to be connected to the recycle line (the inside line).