Unfortunately, if one tries to place any mod-added slab (so far) they are going to be placed horizontally, and on top of that, even bottom slabs seem to have the height of a full block (coordinates on the debug screen are not x.5 but whole numbers. And when these bottom slabs connect to another full block, they make the connected side of that block transparent, because the game thinks they are full blocks.

There are some mods that are incompatible, please figure out which mod is causing problems

Pretty much every mod-added slab I checked had this issue. I checked minegate, colorbricks and a few more and they all showed the same behaviour.