The underlying RDKit libraries used in the RDKit KNIME nodes have been updated to version 2016_03_2. This is now available in the RDKit node nightly builds.
If you want to know what has changed on the backend, the release notes are here: https://github.com/rdkit/rdkit/blob/Release_2016_03_2/ReleaseNotes.md
The previous nodes were using the 2016_09_2 release, so the last two sections of those release notes are relevant here.
In addition to the library change, the nightlies also incorporate a bugfix for the auto-conversion feature for SMILES and MOL/SDF type columns: RDKit cells now generate canonical SMILES from when either RDKit molecules or SDF/MOL cells are converted to SMILES. These SMILES were previously non-canonical.
Note: this change actually happened last week and I didn't notice that something had gone wrong with my forum post until today. :-(