Found the problem and, of course, it wasn't an XPOI bug, but rather a P3D bug. It seems the meaning of the NoZWrite flag has been reversed from P3D 2.1 onward, at least for this kind of semi-transparent objects so, in 2.1+ you have to enable it otherwise some objects will disappear, but that depends on their arrangement on screen.
However, that's not correct and in fact, in FSX objects flagged as such would disappear behind other semi-transparent objects, like clouds.
So, we haven't changed the objects, but updated the installer that will patch all .MDL files when it's done copying, but under P3D 2 only, so we can easily revert the change in case LM will eventually fix this issue. So, for the time being, downloading and installing the updated installer for XPOI will fix the problem with P3D.