Control-M for SAP jobs fail or go Unknown with the following error: Message: SAP0001: Control-M/CM For SAP: 0001 = (135) JCO_ERROR_TIMEOUT: Timeout occurred while logging on to an ABAP system.

Example job log:

18:00:00 4/28/2014 SUBMITTED TO AGENTNAME 5105
18:00:15 4/28/2014 STARTED AT 20140428180000 ON AGENTNAME 5101
18:00:15 4/28/2014 JOB STATE CHANGED TO Executing 5120
19:18:02 4/28/2014 JOB STATE CHANGED TO Unknown 5120
21:18:09 4/28/2014 DISAPPEARED AT 20140428211809. RUNCNT 1. ACCOUNT <Acccount Name> IS UNAVAILABLE 5106
21:18:09 4/28/2014 ENDED NOTOK. NUMBER OF FAILURES SET TO 1 5134
21:18:09 4/28/2014 JOB STATE CHANGED TO Analyzed 5120
21:18:09 4/28/2014 Job STATE CHANGED TO Post processed 5120

Message: SAP0001: Control-M/CM For SAP: 0001 = (135) JCO_ERROR_TIMEOUT: Timeout occurred while logging on to an ABAP system. Remote system [CL3 135.107.70.109/71 40529681] did not reply in 30 seconds.
 

Edit/Add the parameter JcoClientConnectTimeout to the CTMSAP_container_conf.xml in the cm/SAP/data directory.
Set the value to a higher value such as 60

Stop the Control-M for SAP Java Container process, preferably when no jobs are running if possible, with the command:
Unix: sapcmbe.sh stop
Windows: sapcmbe.cmd stop

There is no need to restart the container as it will start automatically on it's own