The Job Scheduler was updated in Sakai 12 to run ScheduledInvocationManager jobs in quartz rather than in a thread.  Most of these were related to future notifications. 

Job Scheduler (11-12)

•  After running all of the database conversion scripts you need to update the Scheduled Invocation Jobs
•  You should login to your system as admin, go to the Job Scheduler tool.
•  Click the Jobs tab, then New Job
•  For the name use "Job Scheduler Conversion" and select the type "Scheduler: Migrate pre 12 scheduler_delayed_invocation jobs to 12 format (Run once)".  There is no additional configuration
•  Click on the button Trigger(0) next to this job, and click Run Job Now.

This process should convert all previous jobs over, it should run quickly as there usually aren't many jobs and finish. This will result in your scheduler_delayed_invocation table being empty.