I seem to recall that enabling the w-buffer made some difference
Yes, I too thought about altering the buffer used. Unfortunately, like an idiot, while I had tried activating the WBuffer in the hopes that it would solve the problem, I did so using a 16-bit display (purely to keep the required specs lower than would otherwise be the case) having quite forgotten that, as such, WBuffer is enabled by default! I grew a brain today and tried turning the WBuffer OFF instead -- the entities in question went back to looking how they should once more, so perhaps it would be useful for you to try your code under similar circustances.
I think I will avoid ortho' projection though, if it makes some entities look odd (your weird skybox, for example) even using the ZBuffer. If you could describe "weird", that would be reet helpful :)