During system startup the DefaultPluginTransformer clears the plugin cache if the system property 'atlassian.plugins.enable.wait' is specified or changed. This occurs midway through the startup and after a number of plugins have already been started.

Why a change of timeout necessitates a plugin cache clear is a mystery, but in JIRA this timing is wrong and can cause

"Caused by: java.io.IOException: Unable to delete file: E:\data\jira\plugins\.osgi-plugins\felix\felix-cache\bundle9\version0.0\bundle.jar"

which causes

"com.atlassian.plugin.osgi.container.OsgiContainerException: Unable to clear OSGi caches
at com.atlassian.plugin.osgi.container.impl.DefaultOsgiPersistentCache.clear(DefaultOsgiPersistentCache.java:75)"

Which causes the spring.timeout never to be written to .properties and so not be set.