You are right, the graph window is rendered by simply drawing the background and then the visible graph elements without erasing the entire view first. The reason for this is simple: there is no way to "erase" anything. Either you draw something or you do not.
In short, the problem is the fact that we allow non-opaque background colors in the first place. We will fix this to support opaque background colors only.
Thank you very much for bringing this to our attention.