In tests I'm finding that 50% of cargo transported is being destroyed, for coal and ore, unless you're also using some other mod that changes stack sizes.
Usually, 100 coal don't fit into a stack. So when you unpack a pallet, 50 are lost. Even worse: nuclear fuel, 99 are lost.
Potential solutions:
(a) Pallets are capped at the natural stack size for that item (and the recipe time is adjusted accordingly). Some items would no longer be packable, e.g. nuclear fuel
(b) You change ore, coal, stone etc. to stack at 100, but that will mess with people's existing bases and screw with balance.