If the the "buildWrappers" section of a job's config.xml (corresponding to the "Build Environment" configuration section) contains a Pyenv Plugin configuration (see snippet below), the entire "buildWrappers" section will not be loaded in the Jenkins web interface (also any configuration that may be present for other plugins). It is not visible in the job's configuration page and is ignored when the job is built.
The configuration file is not changed upon reload/restart. Of course, if the job's configuration is opened via the UI and then saved, it gets deleted (since the UI's Build Environment section is not populated as it was previously configured in the file).
I can not reproduce the issue with Ruby Runtime Plugin version 0.12.
The issue is triggered when the job's config.xml contains the following Pyenv Plugin configuration: