I suggest you ask in the portal forum. If that shows the tools is causing something to fail please let us know - but I believe this to be not specific to the tools.
I managed to find the issue.
When creating the portlet using "new->jboss portlet" in the UI you can only insert init-param value pairs.
I had to include additional entries in the resulting portlet.xml where the portlet-preferences are defined and then the show up in the jboss admin portal.
Maybe an option to be added to the tools later on to be able to do it using the ui.
add a feature request in jira and explain what extra xml you want generated and we'll look into it.