Actually I'm not sure about the AIX level currently but I think they are 7.1.
Anyway, the problem was very simple - we forgot to use "nohup" in front of the command when starting from shell without using the machine-agent script. Normally these agents are started from inittab during system reboot and we just copied the command from there. The working form is:
"nohup <commandFromInittab> &"
Without nohup the agents stop when the user logs off. This wasn't needed on all servers as some servers have probably the WAS user always logged on and that's why I was thinking there is something else wrong now.
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