That scanner helps a a lot, thanks
I'm 100% sure that there are no loops in my design, unless some of the blocks output through sides other than their outputs.
However only the translocator, the following buffer and the first filter are connected to the E-net, subsequent filters are not.
I also played around with the filters and came across what I believe to be a bug.
The secondary (blue) output side is facing downwards by default. If you change it to any other side, even if it doesn't create a loop, it will be disconnected from the e-net, until you reset it to facing downward.
I don't think that this is the source of all of the problems I'm having, so I'll continue playing around with it.
/Edit:
I also just realized that what I was referring to as a "filter" is actually called a "sorter"
super brainfart
face->desk