I have observed the same trait in the playing of some of my students. The people who get mixed-up usually don't have a lot of experience of playing fluently from the unfamiliar score and/or their music theory skills are very limited.
It's like when you read a book in a foreign language where don't know the meaning of the words, it's easy to skip a line or two all of a sudden. However, this usually doesn't happen when you read a book in your native language.
Please note that I'm not talking about the cases when people have special vision conditions - just usual situation when you can't find the right stave quickly and easily when playing organ music.
If you are experiencing similar problems when jumping from one stave to another, this video might be helpful for you to watch.