There is an issue with the FTP inbound channel adapter. It doesn't process files that were already processed before. This is fine, however after a reboot of the application they get picked up anyway.
What we see is that the files are taken from the FTP and put in the local directory put no message is send which would trigger further processing in the integration flow. However since they are kept in the local folder, after a reboot of the application the component has forgotten this and sees a file in the local directory for which it will create a message triggering further processing.