The way you romanize things from the original japanese can vary with a lot of people and there is really no "right" way to do it, but there is a most common way to do it, which is widely accepted.
For example, on Narutopedia, 'Jounin' is spelled as 'Jōnin' ...the line over the 'o' however indicates an elongated sound to the 'o'. So, to simplify it (by writing out the pronunciation, rather then requiring the macron [the line above the letter]), it is then changed to "Jounin" in English.
{{Note: Jonin is wrong, because it lacks the macron (the little line above it).}}
...the same concept applies with 'Chūnin' , where it is changed to 'Chuunin'.
[/Japanese pronounciation and spelling lesson]