Upgrade to 6.4.0.9 failed with errors

We were using JIRa Agile 6.3.5 and upgraded to 6.4.0.9 and after upgrade we see following error in logs and Agile is not usable now.

java.lang.RuntimeException: java.util.concurrent.ExecutionException: java.lang.RuntimeException: Expected exactly 2 rows; the maximum marker row and the lowest ranked row for rank field[id=12600]
at com.atlassian.jira.index.FutureResult.await(FutureResult.java:35)
at com.atlassian.jira.index.CompositeResultBuilder$CompositeResult.await(CompositeResultBuilder.java:82)
at com.atlassian.jira.issue.index.DefaultIndexManager.doIndexIssuesInBatchMode(DefaultIndexManager.java:857)
at com.atlassian.jira.issue.index.DefaultIndexManager.doStopTheWorldReindex(DefaultIndexManager.java:827)
at com.atlassian.jira.issue.index.DefaultIndexManager.reIndexAll(DefaultIndexManager.java:337)
at com.atlassian.jira.issue.index.DefaultIndexManager.reIndexAll(DefaultIndexManager.java:303)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
at java.lang.reflect.Method.invoke(Unknown Source)
at com.atlassian.util.profiling.object.ObjectProfiler.profiledInvoke(ObjectProfiler.java:83)
at com.atlassian.jira.config.component.SwitchingInvocationHandler.invoke(SwitchingInvocationHandler.java:28)
at com.sun.proxy.$Proxy157.reIndexAll(Unknown Source)
at com.atlassian.jira.util.index.CompositeIndexLifecycleManager.reIndexAll(CompositeIndexLifecycleManager.java:56)
at com.atlassian.jira.web.action.admin.index.ReIndexAsyncIndexerCommand.doReindex(ReIndexAsyncIndexerCommand.jav