In conditional probability theory, there exists something called the boy or girl paradox. The paradox shows that the likelihood of an event can be drastically affected by how you know even seemingly innocuous information. I think that observation of the atoms passing through the slit is affecting the search space for the other atoms in such a way that we currently do not understand. This observation while seemingly innocuous has a drastic affect on the distribution which would explain why we see such confounding results. It follows the same logic as this other naturally occurring phenomenon so I think its an avenue at least worth exploring.
An example of the paradox would be if I told you that my neighbor has 2 children and at least one of them is a boy. If I asked you what the probability that their other child is a girl, normally the result would be 2 / 3, but if I know one child is a boy because I spot him in front of a tree then the odds his other child is a girl drops to 1 / 2.