We're using Wrapper 3.5.9 to register our software as Windows Services. In the Services window, if a user clicks on "Restart the service", the wrapper first issues a stop of the JVM and then a start. If the user clicks the "Close" button while the JVM is being stopped the Wrapper, the Wrapper does not longer restart the JVM but simply stops. So far, we have observed this behaviour in any recent Windows OS (XP, Vista, 7, both 32 and 64-bit).
This used to work in an earlier version of Wrapper we were using, namely 3.2.3. Since it takes quite a while till our service is fully up and running, it is essential to be able to close the window and have the service restarted reliably. Although there is an easy workaround (be patient and wait a wee bit longer) this has caused us some headaches in the past.