In reading a book about Fred MacMurray that came out last year I learned that he considered this the worst of his films. While I don't think it's as bad as all that the main weakness of Fair Wind To Java is the casting of Fred MacMurray in a part that was originally intended for John Wayne.
The same author who wrote the novel this film is based on wrote Wake Of The Red Witch which I consider one of John Wayne's best films and certainly his most romantic. After The Quiet Man came out Wayne decided to terminate his relationship with Republic Pictures and Herbert J. Yates. Republic and Yates made most of their money peddling John Wayne to the major studios with him occasionally doing a film for Republic over the years.
Try as he might MacMurray does not cut it as a swashbuckling captain of the China trade. Worse for him was the fact that his leading lady Vera Hruba Ralston was not what he was used to working with. He who made some of the best comedies around with people Irene Dunne, Claudette Colbert, Carole Lombard, Katharine Hepburn etc. found Ralston's lack of talent and professionalism too much.
The villain of the story is Robert Douglas an Australian merchant who also goes around as a Malay pirate with a Lone Ranger mask. This was a true comic book villain I just couldn't take seriously.
The climax is the eruption of Krakatoa where a cache of fabled diamonds are hidden in a temple. That's what MacMurray and Douglas and their respective crews are after. Now considering this is Republic Pictures and not one of the major studios the special effects aren't bad. And the color cinematography is nice.
But if you're beyond the age of 12 it's hard to take Fair Wind To Java all that seriously.