Our captives are constantly trying to comumicate to us. They do so by their actions. In this case, your snake is telling you something, loud and clear.
Lets start at the begining, what you call a nest box is not a nest box, its a box, period. After the female chooses it to successfully nest in, then it becomes a nest box. In this case, your cage substrate proved to be a better nesting area then what you offered. Consider, there is no arguing this, your female is the judge and jury and has rendered her verdict.
When a nesting reptile "makes a mess" out of your intented nesting area, it is saying, this piece of crap is not cutting it. As in, my keeper calls this a nest box, but i surely don't.
Normally a snake does not work a suitable nesting area, they simply and cleanly use it. One burrow going in, nesting quickly and cleanly, then coming out and covering the hole. Anything other then that is degrees of failure.
From the pics, it does seem to all be wet. Snakes do not like wet, they perfer dry and humid. To live in and nest in.
Also, your boxes are, WAY to small, what are you thinking???????? Your approach is very common, its not giving your snake something really good to nest in, your offering something thats just a little better then the cage and hopefully better then the water bowl. In this case, you failed, the cage turned out to be better.
I onced used a funny analogy trying to explain this to varanid keepers. Monitors really use depth in nesting, unlike snakes. But this analogy still applies. One task of nesting is to put the eggs in a safe secure place. "Not where a one-legged robin can dig them up". So you see, you have no depth, or security. I will venture to say, in nature, we do not see snake eggs where the sun shines or where any lite is seen, as in, they nest in the dark.
Please consider, theres different approaches to keeping reptiles, to force them to do what you want OR to invite them to do what you want. To nest them in small lited areas is without question, against their natural behaviors and is forcing them. While we may not have the ability or understanding to nest them like they do in nature, we should give them our best effort. Again consider, REPRODUCTION, can be a life threatening event. Females are willing to die to reproduce, its our job/responsibility to not allow that and give our best effort.
Most natural nests I have seen are from four or five inches deep to over a foot. I imagine that is all about surface temps. It also may be about my lack if digging deeper(to much work). Most of my work here is with montane species and I would think they would not be as deep as low elevation species.
There is much confusion about reptile nests, specially because we have keepers from dry areas and keepers from wet areas. In all these areas the snakes are doing the same thing, only differently. In desert areas, the snakes seek consistantly humid areas(hard to find at times) In wetter areas, they seek the same, only there they are avoiding wettness and water. Here, they are mostly ground nesters, but in wet areas, the ground is far to wet, so they are above ground nesters. Consider, the conditions they seek are exactly the same. I hope this helps, FR