I've earlier set up SubSonic on a Windows system, no problems (even with MP3s in subdirs).
Now I've put it up on a CentOS 4.2 Linux server (no GUI on server) with jre1.5.0_06 / apache-tomcat-5.5.12 / subsonic-2.5.
Works fine, it plays MP3s in the /var/subsonic/mp3 DIR (I had to manually change this as Subsonic 2.5 suggested c:\mp3 even on a Linux system...).
But - when I add any kind of subdirs in the MP3 catalog, SubSonic / Tomcat crashes, end of story. When I remove the subdir and restart Tomcat, everything is OK again.
What gives?