A "BLOCKED" thread is one that has suspended execution as it waits for some other thread to release an object monitor. It is, by definition, not using the CPU. You should instead be looking for threads that are in the "RUNNING" state.
100% CPU is more likely to be caused by GC thrashing than anything else. Turning on GC logging may help you confirm this (multiple "Full GC" reports back-to-back usually indicate a problem, here). An example of what might cause this is something trying to read all of the JIRA issues into memory or something similarly evil.
There really isn't enough information here to help any further with this, but our support team can usually help with tracking down the culprit when something like this is happening.
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