I have uploaded the save.

I just wouldn't expect building orientation to affect operation to the extent that this does.

Along the bottom row of centrifuges, running the kovarex enrichment is (almost) continuous, as the U-235 removed is immediately re-inserted.

The centrifuges across the top ...

I am not sure if this is a bug per-se, \ Factorio Kovarex example.png
attached image is an example of my Kovarex setup.
The centrifuges across the top are unable to unload and pick-up all of the U-235, while the centrifuges along the bottom row are able.

On the top row of centrifuges, it seems ...

my apologies. I had copied and pasted another train logic. The train was waiting to be empty while being filled up with barrels.

I have found a train with "full cargo inventory" criteria seems to get stuck at a train station. The only reason I noticed was 1 solid fuel missing, and that stop was trying to add coal as fuel.