After CMS5 was installed on production server, both the scheduler an indexer stopped working. The .exe for scheduler service is version 5.1.
Evenlog/application logs: Cannot get SchedulerService. Make sure it is started on the localsystem. [Server encountered an internal error]
Problem is constant. Sheduled task does not even start. Running the task manually works as expected.
Had the same problem, here is a FAQ about it.
http://www.episerver.com/en/EPiServer_Knowledge_Center/FAQ_EPiServer_4/Scheduler/Problems-running-the-scheduler-on-machines-with-both-EPiServer-CMS-4-and-5-installations/