Automator turning well-aligned PDF documents upside-down, flipped -- unreadable in OSX?
It must be how you have the PDFs that you want to combine. I have this exact same workflow as an app and it works great and perfectly. However if you have several PDFs that are not all the same orientation then it will do what is happening. 

I don't see any other way of doing it other then manually opening up each one in Preview and using Command L or R to change the right orientation.

Phil