I've read the manual and have started replacing some 3D objects with 2D versions to help with MD3 objects vanishing when moving the camera but I was wondering if anyone knows a fix. If a 3D object is small enough it'll stick around but anything bigger than an average scale table seems to flicker and vanish.

Yes, that is an occlusion (sort of) culling working.
You can either try increasing real radius for decoration or make your models smaller than 64 by 64 by 64