I was able to model the first dice fine, however as soon as I tried making the second one it started disappearing. My CPU and RAM were 100% loaded at the moment, maybe it is somehow connected.
Booleans are very finicky, sometimes the most tiny thing helps, like moving the cutter object up and down a bit, moving it a bit backward of forwards, try reducing the poly count and all those little things you can think of that can trigger the modifier to behave well. As Martin says, flipped normals, interior faces, duplicated vertices, bad geometry overall, try fishing for all that stuff.
This setting seems to have fixed the issue, but loading time was brutal, had to wait like 7 min for it to calculate.
