spring3 + tomcat。
配置文件是自己指定的，只写了一次，所以与默认applicationContext是没有关系的。
Nov 28, 2014 10:46:55 AM org.apache.catalina.core.AprLifecycleListener init
INFO: The APR based Apache Tomcat Native library which allows optimal performance in production environments was not found on the java.library.path: /usr/java/jdk1.7.0_51/jre/lib/amd64:/usr/java/jdk1.7.0_51/jre/lib/i386::/usr/java/packages/lib/i386:/lib:/usr/lib......................
Nov 28, 2014 10:46:56 AM org.apache.catalina.startup.HostConfig deployDescriptor
INFO: Deploying configuration descriptor WebServices.xml
//初始话Context
Nov 28, 2014 10:46:57 AM org.springframework.web.context.ContextLoader initWebApplicationContext
INFO: Root WebApplicationContext: initialization started
Nov 28, 2014 10:46:57 AM org.springframework.context.support.AbstractApplicationContext prepareRefresh
INFO: Refreshing Root WebApplicationContext: startup date [Fri Nov 28 10:46:57 CST 2014]; root of context hierarchy
Nov 28, 2014 10:46:57 AM org.springframework.beans.factory.xml.XmlBeanDefinitionReader loadBeanDefinitions
INFO: Loading XML bean definitions from ServletContext resource [/WEB-INF/serviceBeans.xml]
Nov 28, 2014 10:46:57 AM org.springframework.beans.factory.xml.XmlBeanDefinitionReader loadBeanDefinitions
INFO: Loading XML bean definitions from class path resource [META-INF/cxf/cxf.xml]
Nov 28, 2014 10:46:57 AM org.springframework.beans.factory.xml.XmlBeanDefinitionReader loadBeanDefinitions
INFO: Loading XML bean definitions from class path resource [META-INF/cxf/cxf-extension-soap.xml]
Nov 28, 2014 10:46:57 AM org.springframework.beans.factory.xml.XmlBeanDefinitionReader loadBeanDefinitions
INFO: Loading XML bean definitions from class path resource [META-INF/cxf/cxf-servlet.xml]
Nov 28, 2014 10:46:57 AM org.springframework.beans.factory.xml.XmlBeanDefinitionReader loadBeanDefinitions
INFO: Loading XML bean definitions from ServletContext resource [/WEB-INF/classes/beans.xml]
Nov 28, 2014 10:46:57 AM org.springframework.beans.factory.xml.XmlBeanDefinitionReader loadBeanDefinitions
INFO: Loading XML bean definitions from ServletContext resource [/WEB-INF/classes/datasource.xml]
Nov 28, 2014 10:46:58 AM org.springframework.beans.factory.support.DefaultListableBeanFactory preInstantiateSingletons
INFO: Pre-instantiating singletons in org.springframework.beans.factory.support.DefaultListableBeanFactory@1ebc341: defining beans
..................
Nov 28, 2014 10:47:03 AM org.apache.catalina.startup.Catalina start
INFO: Server startup in 7574 ms
//这里已经启动了
//这里为什么接着就关了，doClose
Nov 28, 2014 10:47:08 AM org.springframework.context.support.AbstractApplicationContext doClose
INFO: Closing Root WebApplicationContext: startup date [Fri Nov 28 10:46:57 CST 2014]; root of context hierarchy
Nov 28, 2014 10:47:08 AM org.springframework.context.support.DefaultLifecycleProcessor$LifecycleGroup stop
INFO: Stopping beans in phase 2147483647
Nov 28, 2014 10:47:08 AM org.quartz.core.QuartzScheduler standby
INFO: Scheduler cleanBean_$_NON_CLUSTERED paused.
//这里destory
Nov 28, 2014 10:47:08 AM org.springframework.beans.factory.support.DefaultSingletonBeanRegistry destroySingletons
........................
Nov 28, 2014 10:47:08 AM org.springframework.scheduling.quartz.SchedulerFactoryBean destroy
..........
//为什么这里取消部署。
INFO: Undeploying context [/WebServices]
Nov 28, 2014 10:47:09 AM org.apache.catalina.startup.HostConfig deployDescriptor
INFO: Deploying configuration descriptor WebServices.xml
------解决思路----------------------
是会有这种情况，没有具体研究过
可能跟部署的应用有关系，也可能跟容器有关系，跟部署的应用的关系大一些。
楼主可以将当前应用从tomcat中移除，启动tomcat试试，看是否重启两次；
换一个其他的应用，放到tomcat中试试，看是否重启两次。