1- On the server doc–click on Server tasks– Agent Managers–You can modify these settings to allow for more agents and longer times for the agents to run. I would increase the number to allow for the times and duration.
2- Go to http://www-1.ibm.com/support/ and search for the following doc #1191036, will give you details on how to debug agents.
3- I would recommend keeping an eye on the agent log analysis to find out what errors are causing the agents to stop.
4- Run fixup -F, Updall -R, and compact -C, at a minumum of twice a week.