In SQL Agent logs for SQL Server 2012 you may see following message that appears every 90 seconds: "Reloading agent settings". It's indeed painful behavior from the user perspectives, and we will address this
issue in nearest Service Pack for SQL Server 2012. For now I can suggest you the the following workaround:
Go to registry on your SQL Server machine and navigate to corresponding SQL Instance registry key:
HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\Microsoft SQL Server\ MSSQL11.YOUR_INSTANCE_NAME\SQLServerAgent
Change registry settings called “AutoRegistryRefresh” from 1 to 0.
The side impact of this: if you change any default settings behavior for SQL Agent, you may need to restart SQL Agent to get it.