I created a new paragraph style with my prefered justification settings. But when I click on it, the text block still flush left rag right. It has all the settings, just not justified. Then when I hit shift command J, then its justified. What am I doing wrong?
Are you creating a named paragraph style? Are you assigning full justification to it within the Paragraph Styles menu, and then saving the style? When the cursor is in the paragraph, is there a + sign on the style name, indicating that an override has been applied to that paragraph? (If the last, click in the paragraph and then click on the Clear Overrides button at the bottom of the Paragraph Styles pane:)
This all comes down to using styles correctly. In short, selecting a paragraph and making changes to it is not using styles, and the formatting will not be persistent as you make other changes to the document.
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After you apply the style to the problem paragraph select it and look at the paragraph styles panel to see if there is a plus sign next to the name of the applied style. If there is a plus showing then hold down the option/alt key while reapplying the style and see if the justification then works. It sounds possible that a previously applied style (which gets removed if you hold down option/alt) may have been applied and is superceding the new one.