Same thing - my clip lands at the end of the file. Got some embedded Python error, too:
Code:
....xmlprocessor.py", line 192, in repairXML
newdata = Opf_Parser(newdata).rebuild_opfxml()
AttributeError: 'Opf_Parser' object has no attribute 'rebuild_opfxml'
after this on right-click
sometimes instead of context menu some dialog box appears - unreadable because filled with cut out fragment of actual Sigil window - forcing me to kill Sigil.
sorry...