Sometimes I have had this get a bit strange. I have had to play with combinations of the orientation of the original and indicate the orientation of the paper in the printer (that would be in Distiller). You may also have to check about the auto-rotate option in the Distiller settings. If you indicate the things you have looked at we might be able to help a bit more.
I think I did the things you mentioned...visited all the settings having to do with page orientation, width versus height dimensions, whether to rotate or not to rotate, and "try, try again."
at least OS X Preview lets one rotate pages; not ideal but for now, a fix.
I am baffled why Distiller does this... sounds like you have to keep trying until something works; that "something" being a magical combo of clicks here 'n' there.
I don't mean to sound bitter, but I've spent hours wrangling with this and it doesn't get better!