I agree with MacD, I do a tonne of box prototyping and run into this all the time, especially when I print UV direct,
The problem with scoring on any digital cutting system, is the scores are not nearly as definitive as if were scored on a cylinder press or a clamshell, what's missing is the matrix.
You can try creating a template out of a thin sheet of MDF and router out the score locations, which would allow the crease wheel a deeper bite into the material, also be aware of the grain direction of your stock, changing the orientation of the grain might help minimize the cracking, as will lowering your total ink coverage.
On a high end piece, with a low quantity situation I've had to switch up from printing direct and print on a economy permanent decal + overlam and mount to the substraight, then cut/score on the backside, that usually eliminates the cracking altogether.