Yes i have seen this if you scale a layer in one axis to below 1% and rotate it. I have also reported it to Adobe as a bug and the response i got from them was that it is know design limitation on AE.
Well there is an easy fix for it, as you also have found, don't scale below 1%, or set the layer to continious rasterize if it doesn't break any effects render order, or if you really need it to scale below 1%, just set the layer to 1% and put an transform effect on and scale further in this effect... or precomp the scaled layer... or just make your solids smaler to begin with so you dont need to scale it so much.
So, there is many fixes for this, so i don't hope Adobe spends too much time to fix this bug ;-)