To configure the stream scheduler to run in multiple applications you need to have the configuration on a per application basis which means NOT having the "ServerListenerStreamPublisher" server listener in the Server.xml.
You will however need to add ServerListenerLoadAndLockAppInstances server listener in the Server.xml and the Properties in the article below.
How to use a server listener to load and lock an appinstance (IServerNotify2)
Note: I have added 2 applications to the loadAndLockApplications Property "live/_definst_" and "live2/_definst_". change these to the application names you wish to use.
<!-- Name of VHost to load the applications on. -->
<!-- Application/AppInstance names to load. Multiple applications are comma-separated. _definst is not required if the default appInstance is to be loaded. Example: live1, live2, live3/myInstance -->
Application configuration should have the following Module and Properties.
Remember the streamPublisherSmilFile will need to be changed to another .stream file in the second application being configured to use the stream scheduler. For example streamschedule2.smil
<!-- The name of the SMIL file that will be used for this schedule. The SMIL file must be located in the application's Streams/StorageDir, which is [install-dir]/content by default. -->
<!-- Pass metadata from the source videos to the stream. Default is true but can cause problems with some players when the metadata has duration values -->
<!-- Log when each schedule switch occurs. If a schedule is set but all items are missing, excessive logging can occur. Set this to false to prevent excessive logging -->