that was caused by the z-buffer, and it was happening even if the submodel was an individual subobject (the infamous turrett bug).
Actually it was happening even when there weren't interesections/disconnections at all, in certain situations, which caused me terrible headaches.
BTW this problem has been fixed many months ago, since IIRC 3.55.
For example, my Fenris has about 140 submodels into IIRC 4 subobjects, and most of those submodels are in the main lod. Actually all the greeblings are disconnected submodels, with a total trianglecount of IIRC ~6500 triangles, when it'd have been over 12k if the mesh was solid....
I don't suggest BTW to use so many submodels, since it can cause the model to be unstable: I spent many hours on the Fenris before getting a stable pof, and I discovered that the amount of submodels can cause the game to crash. Unfourtunately there isn't a clear limit, the Fenris works fine as she is, but she was crashing with 150 submodels, but at the same time I got a model working fine with more than 200 submodels on a single subobject...
Just consider this as an useful strategy sometimes to keep the trianglecount under control...