Now the only thing I could think was that the Atlassian Stash service was getting started before MySQL was completely up, so I went looking at the dependencies:
C:\Users\rweaver>sc qc AtlassianStash [SC] QueryServiceConfig SUCCESS SERVICE_NAME: AtlassianStash TYPE : 10 WIN32_OWN_PROCESS START_TYPE : 2 AUTO_START ERROR_CONTROL : 1 NORMAL BINARY_PATH_NAME : C:\Atlassian\Stash\3.2.0\bin\tomcat7.exe //RS//AtlassianStash LOAD_ORDER_GROUP : TAG : 0 DISPLAY_NAME : Atlassian Stash AtlassianStash DEPENDENCIES : Tcpip : Afd SERVICE_START_NAME : LocalSystem
The dependencies obviously didn’t include the MySQL56.
So I thought the logical thing to do would be to add a dependencies to the MySQL56 service, and then make the Atlassian Stash service dependent on that, so I ran the following:
C:\Users\rweaver>sc config MySQL56 depend= MySQL56/Tcpip/Afd [SC] ChangeServiceConfig SUCCESS
This makes the service depend on MySQL56, and appears to resolve the issue.