We have a web application that began life under LV6 and the Internet Toolkit/G Web Server. There was also a failed attempt at using remote panels thrown in for fun. Now we are running under LV2009 and have migrated to web services fairly well. I don't specifically notice the startup delay you mentioned, but I did also resort to putting a long timeout loop monitoring the server startup (via webserver.app properties) in the application launch frame. Our application starts as a system service, so this delay is probably quite masked for me, thus I didn't notice.
Other issues we faced migrating to web services was the separation between the main application instance and the instance running the web service VI's. This caused some head scratching, but we eventually turned on the main application VI server and called common and global resources held in main memory from application > VI > Call-by-reference wrappers.
Finally, we are now looking at LV2010 and have a big surprise - yet another web server architecture! I am still trying to learn how best to install and configure the Application Web Server for our deployments. I haven't learned very much, but am slowly building up knowledge through the Lava and NI forums. Thanks everyone for posting questions and information!
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James