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The ConversionException: Could not call hudson.EnvVars.readObject() : Invalid reference above is probably unrelated: It looks like my config had invalid references. After cleaning them up, this message disappeared.
However, the IncompatibleClassChangeError: incompatible InnerClasses attribute between "hudson.model.Queue$ItemList" and "hudson.model.Queue" could be the reason for this issue.
I reproduced the issue with Jenkins-1.656 with the following JDKs:
In my case, the "missing" slave is always the first slave in the config.xml, so I would assume that loading a Slave from disk (and creating a hudsom.model.Queue$ItemList) does not work the first time,
but works on subsequent tries.
I've also found that the same error is thrown when creating a new slave on a fresh jenkins (on save / doCreateItem):
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