After upgrading Jenkins and the associated plugins build jobs began to fail when using the publish-over-ssh plugin. In the console output I could find no reference to the files that had been transferring successfully before the update. The work-around to this issue was to put the Source File in its own transfer set. This is contrary to the help section as specified in the Exec Command's help:

"The SSH Transfer Set must include either a Source Files pattern, an Exec command, or both. If both are present, the files are transferred before the command is executed."