test SAP account using CCM test utility
also check in proclog directory cmsap* log file and see if any time out is occurring for the particluar SAP account or any other RFC error ...
Also from CCM for SAP module configuration increase the time out for SAP from 180 to 300
Make sure while you stop your agent u are killing all p_ctmag process on agent , old p_ctmag process can result in delay in job processing and malfunctioning.
then kill SAP process on server make sure to grep the correct SAP process by using
ps -ef | grep SAP | grep <controlm>
hope this will help you .