Comment 8 for bug 1086296

The reason it doesn't happen when toggling live preview with a selection could be the call to 'reselect()' after the undo:
http://bazaar.launchpad.net/~inkscape.dev/inkscape/trunk/view/head:/src/extension/execution-env.cpp#L169

Could this be a limitation of the extension architecture that the current layer is initially not set after the document content is replaced with the output of the effect extension script, and the 'reselect()' causes the current layer to be restored to the layer of the first object in the selected items?

AFAIU changing the current layer is not recording in the undo history, and - if no selection existed - can't be restored by undo (or toggling live preview on/off again)…