We are currently looking into moving to Linux for our ArcGIS Server environment. The last piece I need to implement before we can do this is rewrite our C# SOEs in Java, which I have found fairly easy to do, but I have run into some issues when deploying it to my site.
I am able to export the .soe file, add the extension to my site in manager, but when I add it as a capability on one of my map services, the map service never starts. I was able to deploy the same Java SOE on one of my Windows ArcGIS Servers and the map service starts fine and the SOE functions as it should. I also have tried this using one of Esri's samples and I see the same behavior. I have tried debugging it in Eclipse, but it never breaks since the map service never actually starts. I have also set my logging to DEBUG, but do not see any messages as to why the service is not starting.