Every time we stop our ArcGIS Server 10.2 Amazon Image we need to reconfigure the web adaptor. Anybody have the same trouble or know of a solution?
We had a similar issue, but it had nothing to do with Amazon. So just in case you're having the same issue...
We run the web adaptor in Tomcat deployed as a Windows service. But the Tomcat service always started up faster than the ArcGIS Server service. As it turns out, if Tomcat starts before ArcGIS Server, then the web adaptor is broken until you restart Tomcat.
For us, the fix was to make the Tomcat service have ArcGIS Server as a dependency. From and elevated command prompt I did this:
sc config Tomcat7 depend= "Tcpip/Afd/ArcGIS Server"
(And yes, the weird spacing is absolutely necessary.) This makes Tomcat wait for ArcGIS Server before it even attempts to start up.
After that everything always worked fine after restarts.