Okay, I’m sorry, I thought you were working in Inkscape.
What I would recommend is to stick with one program…either AI CS3 or Inkscape. Whichever one you are more comfortable with, but make sure you are running the most recent update of Inkscape on your computer. (It’s version 0.92 or later. )
If you have AI CS3, and you are familiar with it, go ahead and use it to fix up the file…delete any duplicate lines that you don’t want, make sure everything is copied in that you want, and change the color of any score lines to something different from the cut lines. Then use the instructions in the tutorial below to Save the SVG file.
Try to load that one and see if it still has issues. If it does, it might be something in that Boxes.py script. There are other box generators that might work better if that one causes a problem.