Recently I have been working on a service request where several instances were running, and several technologies were being used, including SOA, BAM, BPEL and others.
At a first glance, this may seem to be a Node Manager problem. But on this situation, the problem was actually at JMS - Persistent Store level. Node Manager can automatically restart Managed Servers that have the "failed" health state, or have shut down unexpectedly due to a system crash or reboot. As a matter of fact, from the provided log files it was clear that the instance was becoming unhealthy because of a Persistent Store problem.
So finally, the problem here was not with Node Manager as it was working as designed, and the restart was being caused by the Persistent Store. After this Persistent Store problem was fixed, everything went fine.
This particular issue that I worked was on an Exalogic machine, but note that this may happen on any hardware running Weblogic.