0.3.3A have 2 reactor ports. One set to input the other to output and the waste is getting ejected into the input port and not the output port.

Separating by 1 block doesn't help for me at least. I am also using 3 different sides of the reactor. Side 1 has controller and energy outputs, side 2 has input and output ports, and side 3 for 2 redstone ports. All cyanite comes to input port (with yellow arrows in texture).

Using version 0.3.3A.

Update: The way i fixed it, is like "giving up and bending to game's will" :p So if waste wants to come to left side port, i change it to output port, and right side port to input. Problem solved.

What i assume is happening, is that game searches from left to right all blocks that contain inventory and puts waste in the first one it finds, even if it is an input port.

I'm having this exact same issue. Didn't realize there was a ticket open and will close mine now. I will add my pictures from mine for the visual

I am also having this problem, not very bad for me in because I check my reactors every few minutes. On a side note I found a very nice CC program to monitor the reactor(s)'s power and output.

Will look into this. I probably mixed up a single argument.

This seems to happen when the input and output ports are adjacent to one another. I separated them by 1 block and Cyanite started to be ejected from the out put port as expected.