This is likely an architectural limitation of the agent. It was designed to be light weight and is largely single-threaded. When dealing with higher numbers of processes in the RFC-2790 section of the MIB, it can cause some communications outages.
In these scenarios we normally recommend disabling of the process table and create process monitors within the empire MIB so that the agent can send traps when a process goes down, rather than depend on polling from the manger. This is a more efficient setup.
Also keep in mind that log monitoring configurations can cause performance issues as well. Smarter usage of regext for a single log/monitor is much more effective than having multiple monitors for a single log.