I have multiple xsd schemas that I want to unmarshall into different packages under the same folder target/generated-sources/xjc. I tried both
General advice: specify your packages in bindings.xjb rather than in different executions with individual generatePackages.
generatePackage does not really work well with multiple schemas.
And please file a bug in
https://java.net/jira/browse/MAVEN_JAXB2_PLUGIN
citing the problem with the multiple schemas and Eclipse. I'll take a look into it.
ps. SO disclaimer: I'm the author of maven-jaxb2-plugin.