If you are using the "Combine PDF Pages" function in Automator, you are using Apple's PDF merging function. Unfortunately, Apple is not doing a good job when it comes to PDF (see for example how PDF forms get corrupted by Apple's Preview: http://khkonsulting.com/2013/06/preview-app-killer-of-pdf-files/).
You will have to complain to Apple about this behavior.
If you want to merge PDF files using Adobe Acrobat, you can use the File>Create>Combine Files... mechanism, which should keep the page rotation correct.
Karl Heinz Kremer
PDF Acrobatics Without a Net
PDF Software Development, Training and More...
http://www.khkonsulting.com