After installing BizTalk server 2013 with SQL 2012 and enabling BAM Alerts services on the machine, you may find BAMAlerts.exe process consumes very high CPU utilization. Moreover, if BizTalk and SQL are installed on the same box, BAMAlerts.exe and SQL service processes will result in a 100% CPU symptom.
When being installed with SQL 2012, BizTalk 2013 starts to use Database Mail feature of SQL 2012 to implement BAM Alerts (SQL 2005 Notification Service is still used for BizTalk 2013 installation with SQL 2008 R2). We have confirm the high CPU symptom is a product issue and are working on the fix of it now.
If you also meet the same problem and look for a solution, please contact Microsoft Support to request the hotfix or wait for the next release BizTalk 2013 cumulative update package.