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I have set Word Wrap as follows:

Configure > Preferences > Document Classes > Default > Word wrap long lines

With Word Wrapped Text: Save with no breaks in lines

selected. However, when I open files with long lines, Word Wrap does not apply to the file, and I have to set it manually by using the toolbar button.

Is there another setting that might be interfering with this?

Yes: each other document class (i.e. "Text"). Based on the file(type)s you open you will also have to configure those classes.