Well this was an easy fix... When FMS 13 installed, it found and mounted the files from FMS 12's data folder. Everything seemed to work until I tried to set up the schedule.
The fix was to remove/delete all of the files and have FileMaker Pro upload new copies so that they were installed through the standard process. This fixed it. My guess is it was file/folder permissions. FMS 13 had a new fmserver ID.