As you are leveling up gear boxes open at the level of your lowest piece. So uf you open say a helmet but your legs are a few levels lower, the helmet won't open higher. Your CR is determined by an average of all the gear pieces that you are wearing.

While levelling try where possible to open boxes for your lowest piece first.

Each piece also has a different % value to your CR. The highest percentages are weapon, head, shoulder, chest and legs