- Have you configured the Flatfile Disassembler in the custom Pipeline with the correct schema?
- Have you deployed the entire application from the Solution, and not from each Project?
- Have you Selected the proper Pipeline from the drop down in your Receive Port configuration?
- Have you restarted the Host Instance for the Application to be sure your changes have taken effect?
I'd ask about Folder permissions, but apparently that's fine or you wouldn't get an XML file to work.