If after a sync you get the error 'Songs missing from your cloud service.' it indicates that certain songs marked for download couldn't be found on your cloud service. Typically this is caused by file not yet being uploaded yet. The regular solution is to wait for your cloud service to finish syncing and Cloud Tuner will find the files after its next sync.
In rare circumstances, this error indicates that the song/s you are trying to sync aren't located on your cloud service. This can occur if you're using an iTunes library without the options 'Copy files to iTunes Media folder when adding to library' or 'Keep iTunes Media folder organized' disabled in the advanced preferences of iTunes. There's more information about keeping your iTunes library organized over at Apple Support: Locate and organize your iTunes media files
In circumstances where your computer has finished syncing and you continue to receive this error, the sync log will be able to tell you what files failed to be found.