I could be wrong, but the numbers shouldn't be colored at all, as I don't believe there is any option anywhere to edge ID number colors. My first thought on that would be to check your ink cartridge and make sure it hasn't expired. I didn't even know they did that until after having to go through a lengthy tech support chat on why my relatively new printer was printing out blues and greens instead of black.
As for the numbers being too close together, there is an option under "Settings," then "other settings," and then the "others" tab that says "place edge ID inside of face." If you check that box, it will put the numbers on the flap instead of on the model itself. The downside here is the corresponding face that will not have a flap will just have that number printed out floating in the middle of nowhere next to that face. So you'll have to either remember those numbers, or have to write them in yourself. Another downside to this it that the numbers being printed on the part rather than the flap gives you a center point to line up the two pieces.
Please note that there is a "Help for Misc." thread that is meant to field any questions you might have that doesn't fit into any of the other categories (i.e. paint, foam, molding, etc.). Technically this one could fit into the "Help for Pepakura" thread, as well. Just helps keep things more organized and clutter-free when questions are posted in specific help threads rather than starting a new thread just to ask a question.
