@Everyone, Mendix has confirmed that my problems is caused by the changes in MX5.8 and that they will try and implement a fix in the upcoming 2 months.
For now the workaround is to filter the following tags:
<soap:Envelope>
<soap:Body>
This is of course only the case where you parse a XML document and not when parsing a web-service response directly. My case requires this work around due to a bug in the output that I was already filtering pre-parsing stage.