I believe this is an issue with the way SE moves the ore in conveyors and refineries. If your refineries don't have a conveyor connection each SE tends to just load the first one and doesn't balance between the two. Try adding a second conveyor connection for the second refinery directly off of the mine as well. This issue tends to come up a lot in SE when you chain refineries together instead of giving them their own conveyor lines. As far as I can tell this is not related to the script, just a weird SE thing. Hope it helps.

And yes, I realize this was an old post, just wanted to throw out an answer for anyone who may still run into this problem.