I've had the same problem that you had with the breeding boxes. The first one I got for free from a breeder, but by the looks of things he must have drilled bigger holes in the bottom for bigger fry. I went to a pet store and bought a box that had the V insert also. When I noticed tiny fry in my tank, I put her & the fry in the box. They swam up through the V too! I thought that the reason for the V insert was to keep them from swimming back up. So I finally gave up on the whole breeder box idea and set up a 5g tank and put the fry in there.
I would agree with the others and just let her have the babies in the tank. If there are enough hiding spots they will survive, or you can look at it as the "Natural Selection" theory. Only the strongest and best fit will survive.
A few days after my first guppy popped, my other one did also, and I found the fry hiding in a driftwood ornament that I have (they are pretty much camouflage in it) and the plant that I have. There are also some brave ones that like to swim with their mommies. So far I haven;t had any that have been eaten. The mothers have tried, but they are too quick for them.
As for the deaths that you had, I don't really have any suggestions. It's pretty disappointing for that to happen though. Did you clean the small tank with anything before adding the water? Sometimes you may think that you got all the soap out but there may still be traces. Since the fry are so tiny it could have been a number of things. As others have said, it may have been stress, but I haven't had this situation happen to me before.
Best of luck in the future!