8.1.48 is going to support -Dignition.synthetica.customXml=... system property that you can point towards a synthetica XML file, such as one containing this:
<synth>
    <defaultsProperty key="Synthetica.popupRobot.enabled" type="boolean" value="false"/>
</synth>
which can be used to set the Synthetica.popupRobot.enabled property, as well as any other Synthetica UIManager property.
I'm not sure if the popup menus appearing in random places are related to this or not.