Another possibility is they are getting sucked into the filter in the main tank. Do you have a sponge prefilter on the intake?
Thank you for mentioning this.If you feed low protein to your shrimp, especially in Spring, you can most definitely have predation. I have seen it for sure a couple of times and have heard it many more. I do agree that predation was not likely the cause of the entire brood being lost. More than likely it was starvation or some other environmental condition. The breeder box allows you to target feed the babies and with diligence have good success. For me, I use the marina boxes to selectively breed/mate my shrimp...then put berried mothers back into the tank to hatch and raise the babies. That is unless it is a special selective brood which I would like to isolate.
Anyway, great job Master!