I was having the same problem too., it was driving me mad. I managed to fix it in Preview by adding in the landscape pdf pages to the portrait pdf pages, rearranging and resaving. This is Preview's instructions:
- Add a page to a PDF: Choose Edit > Insert, then choose Page from Scanner, Page from File, or Blank Page.
- Move pages in a PDF: Choose View > Thumbnails or Contact Sheet, then drag the pages to their new location.