I'm no master coder or scripter or anything, but here is an idea that could really help out a lot, and it can be explained by logic.
You can make the bot click the boxes closest to coordinates (50,50) (Middle of the screen) because, your ship in dark orbit is ALWAYS in the middle of the screen. Making this script would mean your bot would always click the boxes closest to your ship, then after continue on to the box trail.
Now this really helps out because it saves a couple seconds in travel time, and can make your bot clear out box trails, (big patches of boxes) easily and more logically. Normally when I watch the bot for a couple of minutes, it goes for a far box, then come back in the direction my ship came from, to collect a box that was closer in the first place, wasting a couple seconds that could be used for traveling or collecting another box. I feel like it is an easy fix and can be fixed in a line or two of scripting.
It isn't a bug, and doesn't necessarily need to be adjusted, by just my two cents, again just constructive advice, and I mean no harm.