There's an option in there that controls the page turn direction for languages that use right-to-left (RTL) text. I think iBooks is just about the only reading system that actually supports the feature correctly. It sounds like for some reason Calibre incorrectly used that feature in the EPUB when converting it.
To fix this:
- Extract the EPUB (it's just a ZIP file, basically) and open up the .opf file.
- Look for the page-progression-direction attribute on the spine element and change it from rtl to ltr (or remove it).
- Recompress the ZIP archive in a way that ensures that the MANIFEST file comes first.