Reloading Agent Settings appears in SQL Agent Logs every 90 seconds | Microsoft Connect

One of the things you may want to do as soon as you install SQL 2012 is disable the auto refresh feature of SQL Agent, which will fill up your agent logs with superfluous messages.

We investigated this issue and it's indeed painful behavior from the user perspectives, we will address this issue in nearest Service Pack.
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.

Reloading Agent Settings appears in SQL Agent Logs every 90 seconds | Microsoft Connect