I can see a few possibilities that could force this behavior in the switches: some STP issue in the stacks or in the topology; some configuration that is missing in the stack configuration; a software bug in the running version. I don't know the stack configuration of the switches you have, but even in the latest hardware versions this problem occurs concerning the stack configuration and STP issues.
I would try the following steps:
1. Run a network discovery using 3Com Network Director and generate some topology and misconfiguration reports in order to check if there is something that is missed on the configuration and topology.
2. Create a lab using the same software version, using a topology similar to the environment you have, and check the stability of the stacks. If does not occur any problem, check the traffic flow. If the problem occurs, perform a downgrade one version back and perform the tests again.
3. If you have a flat network, consider to create new segments, optimizing the traffic and reducing the size of broadcast domains. Maybe these switches are learning a large amount of MAC addresses, what will causes a crash in the stack removing the switch from it.
HTH