InfoPath supports forms with file attachments by encoding the attachement as base64 and including the following PI
at the top of the XML document to indicate that a file has been attached to the document.
WSS adapter works with InfoPath forms with attachements by making sure that it does not add/remove/update any of the PIs that are related to file attachment. If the files are attached to the form in InfoPath then the PI should be there because InfoPath adds it. If the files are attached by your orchestration or some component other than InfoPath, then the orchestration/component needs to add the PI explicitly. The adapter cannot know if a file attachment is included in the form (unless the PI is present in which case there's nothing to be done) so it will never add the PI. You can add the PI explicitly in your orchestration using a construct like this:
msg(XMLNORM.ProcessingInstructionOption) = 1;
msg(XMLNORM.ProcessingInstruction) = "<?mso-infoPath-file-attachment-present ?>";
So, whatever component attaches the files to the form needs to also add the PI. WSS adapter will preserve the PI if it's in the document, but it will never add such a PI to the XML document.