Copy a single word from the page.
Put the caret at the end of para "1".
Hit SHIFT+ARROW-DOWN to select para "2".
Right in the selected para "2" and select "Paste". Allow clipboard access so it gets executed.
The "span" entry will show in the elements path, and the bookmark can be confirmed in the source view.
Confirmed with CKEditor 3.2.2. Works well with version 3.2.1.
WFM now in trunk, any trick to reproduce?
I was able to reproduce it till CKE 3.3.1. From CKEditor 3.3.2 it seems to work fine.