When you print a multi-page two-sided document with mixed page orientations only one binding direction can be set for the entire document.
Assume that you print a multi-page document with Print on Both sides selected and have a mixed page orientation within the document, for example a few pages of Portrait and a few pages of Landscape. You then choose to format the second side to flip over (like a notebook) or flip up (like a calendar) and depending on the orientation, flip on long edge or flip on short edge. Word will then follow the same rule throughout the document for all pages in a duplex job. This will cause the second side of the document to appear as if printing incorrectly if the second side of the document has a different orientation.
If you choose to format the pages so that it will flip pages like a notebook, it will cause the page to flip on the long side in portrait, which instead causes it to flip like a book. It will also flip on the landscape, causing the text to be upside down. As the rule states, flip up or flip over does not discriminate between which orientation the page is in. This will cause the portrait pages to flip upside down, but the landscape pages will read like a book. This is by design and is printing literally as it is stated in the print settings.
Separate the duplex job which has combined orientation settings in it, and change the Flip settings to match the page orientation.