It sounds like we had the same problem. We have ArcGIS Server 10.1 on Linux. We installed the Web Adaptor on it's own VM. Every time that tomcat was restarted, the Web Adaptor configuration settings disappeared, and therefore the AGS was not accessible through the web server until we manually went in and reset everything. We ended up getting rid of the Web Adaptor in favor of having Apache handle routing. For us, the Web Adaptor was just an added point of failure.