You can see the black squares when backface culling is disabled, but even with it on you can see a weird coloration on some of the object. With shadeless enabled you can’t see them at all. And it only shows up when transparency is on.
It is a bug for transparent objects that are behind other transparent objects(or are parts of the same object). If it is using transparent texture, than in textured part other objects using the same method(or just transparency) are visible. This doesn’t affect alpha clip. However, exporting aplha blend transparency objects as .fbx and than importing them usually fixes it for me.
He was more worried about that you can see the back of through the texture untransparent parts. This problem doesn’t act if you use alpha clip, but otherwise…
You guys are right, they’re not black squares at all, that was just the lighting I guess. Alpha clip and alpha sort seem to do the trick. Turning transparency to raytrace also works, but then there’s a different problem. Anyway, thanks for the help.