A case was open to BMC case CAR00034959 .
Jobs are executed correctly, but when the sysout is analysed by the tracker, there is some internal problems, and the tracker run on itself.
If you run a prstat or top utilities, you could see tracker using a lot of memory and doesn't free it.
So In fact your job wait in executing mode the total return from the tracker, and it could wait for a long time.
If you try to stop your agent, p_ctmag could be stopped, but not the p_ctmat. To start again correctly your agent you must kill p_ctmat process.
Workarround before Fixpack:
Install from scratch your Unix Agent and deploy only the Fixpack 1.
It should be run correctly
Solution from BMC:
If you need to apply FP2, It's recommend that to set the 'BUFFERED_DBGLVL 0' on the agent CONFIG.dat file and restarting the agent. It should solve the problem. Alternatively, you can wait until Fix Pack 3 of the Agent is released where this problem will be resolved.