Two excellent notes on getting your Linux box to work on the normal DIIOP port:
First: Domino Access to Java objects, part II:
And the most helpful:
Also, I found I could not have multiple FQDN's on the basics tab. I also found ben poole's web site very helpful: www.benpoole.com.
Also, refer to my other notes in this forum on how I finally was able to get Domino 6 clustering and Linux-HA to work together. I put that there because I figured if it frustrated me, it probably did you, too.