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Hi. Sorry for the delay.
Oleg- The slave is nothing out of the ordinary, just a simple, Java Web Start slave. It is not happening with the "same" slave always, just one that gets disappeared. If I have 4, and jenkins is restarted, 3 appears. If I restart again, I'm left with 2. My feeling is that it depends on the order in the xml configuration.
John - No, it was a new installation. I recently updated to 1.554.1 LTS, and removed the webapps folder. The issue is still there. I'll try removing the cache directory, though. It is a Windows machine, so I'll see where that folder is.
Daniel- Yes, there is. It says: hudson.model.Hudson IncompatibleClassChangeError: incompatible InnerClasses attribute between "hudson.model.Queue$ItemList" and "hudson.model.Queue.". But I'm not too convinced that it is related, as Oleg said.
While troubleshooting the issue, I found out that the missing slave configuration was in the jenkins' config XML, and discovered that hitting "Reload configuration from disk" makes the slave to appear again. As a workaround, I created a Groovy post-init script (https://wiki.jenkins-ci.org/display/JENKINS/Post-initialization+script), that calls the Reloading function.. So after restarting and just after finishing the initialization process, my jenkins reloads the configuration again, making the slave to appear again. It is a dirty workaround, but has been working for several weeks.
My suspicion is that it is a problem when running Jenkins on IBM Java, maybe even specific with IBM java versions.