Can you please modify the fiddle in order to demonstrate the issue.
The issue happens when we are using Object3D.clear() method. In this case CSS2DObject element persists in the DOM tree. The correct behavior in this case should be similar to other objects, they are removed from the scene on the next render.
Here is the example of the problem (line 76).
UPDATE. Found the hacky way to solve this by using the remove event here. Thanks Mugen87.