Your PDF is a very good quality. I tryied to make some orgimi dice with Gimp and I don't have the same quality . Can you tell me how you design them to have such quality ?
I just took the original origami 3 cm pdf & extracted the image. Then I took out the background, re-sized it, added a new background layer under the lines. Then I added the dice face under the line layer. When I was finished I then flattened them & saved them as a pdf. I use photoshop not gimp, it's an older version but it works, I can't afford to upgrade & as long as it works I'm happy.