I had the same problem (using the plugin you mentioned in combination with
ActiveBPEL Engine 4.0 and Eclipse Europe). The problems occures because
either the plugin or the Eclipse Designer itself has trouble dealing with
<import>-tags within the WSDL-files need for partner links.
So if this is an options for you, delete all <import>-tags from the
WSDL-files used for your partner links. You should be able to publish the
BPEL Process afterwards.