Basically, when unioning several cubes very weird stuff happens:
This is done with 5 cubes, each 9x9x9 ( Size doesn’t matter )
The effect isn’t as dramatic with cubes placed in a grid, but still very broken:
( Screenshots have ShowDecompositionGeometry set to true to show the physics mesh )
You can check it out here ( Edit mode )
EDIT: Just noticed some parts are also missing visually from some of the unions
I think your problem is similar to that explained on a few other topics. The accuracy of collision geometry breaks down as your total union gets larger and the parts whose physics you care about get smaller relative to the entire size.
What about some of the cubes not being rendered, I assume that is unrelated to the physics mesh?