Well, two hours and I finally figured out what was wrong. It was the mimetype for each contact property (or what have you).
Basically, because we seem to only be able to query the Data.CONTENT_URI, we need to validate against the MIMETYPE for the particular property. In my case, the following snipped fixed it :D
while (orgCursor.moveToNext())
{
String organisation = orgCursor.getString(orgCursor.getColumnIndex(CommonDataKinds.Organization.DATA1));
String title = orgCursor.getString(orgCursor.getColumnIndex(CommonDataKinds.Organization.DATA4));
String MIMETYPE = orgCursor.getString(orgCursor.getColumnIndex(CommonDataKinds.Organization.MIMETYPE));
if ((organisation != null) && (title != null)&&(MIMETYPE.equals("vnd.android.cursor.item/organization")))
{
orgObj.put(organisation, title);
Log.v(TAG, "org is " + organisation.toString() + " title is " + title.toString());
}