That was going to be my question... have you had any reply to your question?

The Happy DBA!!!

This is an issue with 2012 and MS is aware of it. Do not apply the registry fix proposed by MS support. More info here:

http://connect.microsoft.com/SQLServer/feedback/details/729700/reloading-agent-settings-appears-in-sql-agent-logs-every-90-seconds

I was in the same situation, but what helped me was to run a full backup right before I attempted to shrink the file. It did work for me.