I'm not sure exactly what causes this, but part of the problem is probably that after the clone, you have two #f1's. It might work better to define the filter in a single <svg>
that you never clone, and have the cloned <svg>
just reference that.
<svg xmlns="http://www.w3.org/2000/svg" version="1.1" height=0px width=0px id="defs">
<defs>
<filter id="f1" x="0" y="0">
<feGaussianBlur in="SourceGraphic" stdDeviation="15" />
</filter>
</defs>
</svg>
<svg xmlns="http://www.w3.org/2000/svg" version="1.1" height=100px width=100px id="rect">
<rect width="90" height="90" stroke="green" stroke-width="3"
fill="yellow" filter="url(#f1)" />
</svg>
See this update fiddle.