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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$ItemList" and "hudson.model.Queue" could be the reason for this issue.
I reproduced the issue with Jenkins 1.554.3 (LTS), 1.565 and 1.570 with the following combinations.
The issue does not occur on Jenkins-1.532.2 (LTS).
In my case, the "missing" slave is always the first slave in the config.xml, so I would assume that loading a Slave from disk (and creating a hudsom.model.Queue$ItemList) does not work the first time,
but works on subsequent tries.
I've also found that the same error is thrown when creating the first slave node on a fresh jenkins instance (on save / doCreateItem):
The slave is saved nonetheless.
Subsequent slaves can be created without this error.