That's odd. It should have shown up when I asked you to check "/usr/sap/EP1/J02/j2ee/cluster/apps/Nakisa/OrgModeler/servlet_jsp/OrgModeler/WEB-INF/lib/sapjco.jar" earlier. Still at least you've got to the bottom of it now 
The cds.log generation uses the log4j component (an Apache logging module). For the command line logging sometimes the initial file copy that takes place doesn't copy the log properties files in (I've never spotted a particular pattern of when it works and when it doesn't). The first run however almost always misses the properties.
Check in the .../root/WEB-INF/lib/log directory for the *log*.properties files that exist in the .../root/log directory (forgive me if my upper/lower case path references donot match exactly). If they do, try restarting the listener and see if you still get the error. If they are not there, copy them in and restart the listener.