Creating Epubs via converting PDF problem

Hi, already made a thread, but it was sort of confusing, and they merged everything into one ipad discussion. don't know if it was lost or not.

anyway, I'm scanning my coaching books (some have pictures) into PDF files using my scanner. I was flipping the book the opposite way when I had to scan the other page, so I did not have to flip the book all the way back and damage the binding.

When I put all the files together in preview, I rotated the files that were "upside down" because of my method of scanning, cropped out what I didn't want, and then saved.

Converted these files using Calibre and loaded them onto the ipad...and they still show some pages (every other) as upside down. when I click on the original PDF file it shows the file with all the corrections made and everything is just how I want it.

anyone have any idea of whats going on? I would have to have to rescan my books that I already did.