I get many repeat errors like in the attached stdout_<date>.log file.
Most often is $atl_token is not a valid reference.

Excerpt:

2010-06-24 14:59:50,304 http-443-Processor19 WARN [velocity] org.apache.velocity.runtime.exception.ReferenceException: reference : template = secure/admin/minyaa/MinyaaCore.vm [line 13,column 153] : $atl_token is not a valid reference.
at org.apache.velocity.runtime.parser.node.ASTReference.render(ASTReference.java:277)
at org.apache.velocity.runtime.parser.node.SimpleNode.render(SimpleNode.java:230)
at org.apache.velocity.Template.merge(Template.java:256)
at org.apache.velocity.app.VelocityEngine.mergeTemplate(VelocityEngine.java:450)
at com.atlassian.velocity.DefaultVelocityManager.getEncodedBody(DefaultVelocityManager.java:77)
at com.atlassian.jira.plugin.webwork.JiraPluginWebworkVelocityServlet.service(JiraPluginWebworkVelocityServlet.java:46)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:803)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:269)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188)
at org.apache.catalina.core.ApplicationDispatcher.invoke(ApplicationDispatcher.java:679)
at org.apache.catalina.core.ApplicationDispatcher.processRequest(ApplicationDispatcher.java:461)
at org.apache.catalina.core.ApplicationDispatcher.doForward(ApplicationDispatcher.java:399)
at org.apache.catalina.core.ApplicationDispatcher.forward(ApplicationDispatcher.java:301)
at com.atlassian.jira.web.dispatcher.JiraServletDispatcher.service(JiraServletDispatcher.java:248)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:803)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:269)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188)
at com.atlassian.core.filters.HeaderSanitisingFilter.doFilter(HeaderSanitisingFilter.java:44)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188)
at com.atlassian.jira.web.filters.AccessLogFilter.doFilter(AccessLogFilter.java:73)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188)
at com.opensymphony.module.sitemesh.filter.PageFilter.parsePage(PageFilter.java:119)
at com.opensymphony.module.sitemesh.filter.PageFilter.doFilter(PageFilter.java:55)
at com.atlassian.jira.web.filters.SitemeshExcludePathFilter.doFilter(SitemeshExcludePathFilter.java:38)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188)
at com.atlassian.seraph.filter.SecurityFilter.doFilter(SecurityFilter.java:204)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188)
at com.atlassian.seraph.filter.TrustedApplicationsFilter.doFilter(TrustedApplicationsFilter.java:120)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188)
at com.atlassian.seraph.filter.BaseLoginFilter.doFilter(BaseLoginFilter.java:138)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188)
at com.atlassian.util.profiling.filters.ProfilingFilter.doFilter(ProfilingFilter.java:132)
at com.atlassian.jira.web.filters.JIRAProfilingFilter.doFilter(JIRAProfilingFilter.java:16)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188)
at com.atlassian.jira.web.filters.ActionCleanupDelayFilter.doFilter(ActionCleanupDelayFilter.java:47)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188)
at com.atlassian.jira.web.filters.RequestCleanupFilter.doFilter(RequestCleanupFilter.java:50)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188)
at com.atlassian.johnson.filters.AbstractJohnsonFilter.doFilter(AbstractJohnsonFilter.java:72)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188)
at org.tuckey.web.filters.urlrewrite.UrlRewriteFilter.doFilter(UrlRewriteFilter.java:350)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188)
at com.atlassian.gzipfilter.GzipFilter.doFilterInternal(GzipFilter.java:81)
at com.atlassian.gzipfilter.GzipFilter.doFilter(GzipFilter.java:51)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188)
at com.atlassian.core.filters.AbstractEncodingFilter.doFilter(AbstractEncodingFilter.java:33)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188)
at com.atlassian.jira.appconsistency.db.DatabaseCompatibilityEnforcerFilter.doFilter(DatabaseCompatibilityEnforcerFilter.java:39)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188)
at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:213)
at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:174)
at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:525)
at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:127)
at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:117)
at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:108)
at org.apache.catalina.valves.AccessLogValve.invoke(AccessLogValve.java:548)
at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:174)
at org.apache.coyote.http11.Http11Processor.process(Http11Processor.java:874)
at org.apache.coyote.http11.Http11BaseProtocol$Http11ConnectionHandler.processConnection(Http11BaseProtocol.java:665)
at org.apache.tomcat.util.net.PoolTcpEndpoint.processSocket(PoolTcpEndpoint.java:528)
at org.apache.tomcat.util.net.LeaderFollowerWorkerThread.runIt(LeaderFollowerWorkerThread.java:81)
at org.apache.tomcat.util.threads.ThreadPool$ControlRunnable.run(ThreadPool.java:689)
at java.lang.Thread.run(Thread.java:619)