For anyone else that comes across this problem, here is what I found;
It turns out that saving through the Homepage refused to work, however I did successfully save Instance Data when the widget is loaded through the Communities mechanism;
JavaScript for saving (.save calls a callback function, but not necessary):
if(this.inCommunity)
{
this.iContext.getiWidgetAttributes().setItemValue("instance",contentToSave);
this.iContext.getiWidgetAttributes().save(dojo.hitch(this,this.dashboardSaved));
}
Loading saved data:
this.instanceData = this.iContext.getiWidgetAttributes().getItemValue("instance");
Widget definition (in widgets-config.xml)
<widgetDef defId="Dashboard" description="MyDash" modes="view edit" url="/Dashboard.xml" uniqueInstance="false">
<itemSet>
<item name="instance" value=""/>
</itemSet>
</widgetDef>
Dashboard.xml
<iw:iwidget xmlns:iw="http://www.ibm.com/xmlns/prod/iWidget" iScope="Dashboard" supportedModes="view edit" mode="view" allowInstanceContent="true">
<iw:resource uri="./dashboard.js"/>
<iw:event id="view" handled="false" onEvent="onView"/>
<iw:event id="edit" handled="false" onEvent="onEdit"/>
<iw:event id="onRefreshNeeded" handled="true" onEvent="onRefresh"/>
<iw:itemSet id="attributes" private="true" onItemSetChanged="itemSetChanged">
<iw:item id="instance" readOnly="false"/>
</iw:itemSet>
<iw:content mode="view">
<![CDATA[<div id="RootWidget"></div>]]>
</iw:content>
<iw:content mode="edit">
<![CDATA[<div id="RootWidget"></div>]]>
</iw:content>
</iw:iwidget>