It seems like you're encountering an issue where the paper size of your Word document is not being preserved when printing to PDF. This can happen if the PDF printer settings are overriding the document's settings. Here's what you can try to resolve the issue:

Check Printer Settings: When printing to PDF using the native MS Print to PDF utility, check the printer settings to ensure that the paper size is set to 6x9 inches. Sometimes, the default paper size settings of the PDF printer may be set to letter size (8.5x11 inches), which can override the document's settings.

Page Setup in Word: Double-check the page setup settings in your Word document to ensure that the paper size is set to 6x9 inches. Go to the "Layout" tab, click on "Size," and select "More Paper Sizes" to specify the custom paper size if needed.

Print Preview: Before printing to PDF, use the print preview feature in Word to verify that the document appears correctly with the 6x9 inch paper size. This will allow you to see if any adjustments need to be made before creating the PDF.

Use Different PDF Printer: If the issue persists, consider using a different PDF printer utility or software to print your document to PDF. There are several third-party PDF printers available that may offer more customization options for paper size.

PDF Printer Properties: When printing to PDF, check the printer properties or preferences to see if there are any options related to paper size. Ensure that the paper size settings match the document's settings.