The pop-up pick lists calculate their DocNodes when the pick list is shown, and then insert them into the document later unchanged. This means that if the document changes between those times, e.g. a library is loaded or results imported, then the inserted nodes can be out of sync with the rest o the document.

To avoid this, the picking algorithm will need to allow for the picked nodes to have ChangeSettings() called on them during the ModifyDocument() call to ensure the inserted nodes are consistent with current document settings.

Skyline issues have moved to GitHub Issues at https://github.com/ProteoWizard/pwiz/issues
Issues will be ported as necessary for active work.