One of the challenges of making good box joints is clamping during glue-up. You can't clamp directly on the joints (because the fingers stand a bit proud) so we are forced to put clamping pressure next to the joint which introduces torque and pulls the sides in a bit. For 1/2" or thinner wood, this can cause small gaps in the box joint plus it distorts the sides of the box a bit and makes it hard to use an inside square to check the squareness of the box. See the attached picture for an example.
The solution to this problem is to use clamping cauls that allow you to place pressure directly on the fingers. There are commercial products that do this. In particular Rockler has them for 1/4", 3/8" and 1/2" finger sizes. The cauls are reasonably priced though you need a band clamp as well. While they do work, the fingers are open and, even with moderate clamping pressure, they press marks into the box fingers. See the attached picture. The wood is cherry and the mark was made just by squeezing with my arthritic fingers. Needless to say, this is not desirable.
So, the answer is to make clamping cauls yourself. It's not hard and if you have an Incra LS Positioner, it's really easy. I've put together a tutorial on how to do this with the Incra LS Positioner
using Rob Lowrie's pyRouterJig software.
If you don't have an LS Positioner or similar, you can still make cauls. Basically, it's very similar to making box joints with fingers that are 1/8" deep. The caul fingers should be around 1/16" narrower than the box joint fingers. You cut them out of a 3 1/2" x 1" thick piece of hard wood. The length should be about 1 1/2" longer than the joint you are clamping. See the pictures to understand the process. It should be easy to modify your box joint jig to do this. But, it should be possible to make just using a dado blade and miter gauge - precision is not needed. You might want to look over the above tutorial to get a better idea of the process.
Note that the measurements in the attached pictures are for custom finger spacing - don't use those measurements for a standard spacing box joint.
The final picture has been posted before but it shows the results of getting direct, square and even clamping pressure via cauls on box joints.