I am working with RIM on this issue as I am experiencing the same thing after upgrading to SP6 from 4.1.4 on Friday. The 100% CPU is being by the BBAgent.exe, BBController.exe and services.exe (this service should always be at 0% unless processing a stop/start of a service. I have seen that once I stop/start the BBController service the CPU for the entire server returns to normal.
I am have uploaded my MS app log and today's BB log to RIM. I am still on hold with them and will provide further details once I have them.
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