Following a recent update to the RDKit binaries, we have made a minor update to the existing MMP nodes to return the correct behaviour for molecules containing existing or newly created double bond geometry during the fragmentation process. If you have used the fragmentation nodes since 15th May 2017 (and have updated RDKit since then too) then you may need to revisit the results following this update.
Brief description here - https://tech.knime.org/book/vernalis-release-notes-changelog
Fixes problems introduced by the following changes to RDKit:
https://github.com/rdkit/rdkit/pull/1202
and the change to dative bond representation discussed here:
https://github.com/rdkit/rdkit/pull/1190
(The update should try to figure which version of RDKit you have installed for this latter issue - if you see any issues then please let us know!)
Steve