Hi,
This means there is some problem clearing the cache. When you touch Web.config it recycles the app pool and this clears the site map cache.
This should not be neccessary and probably indicates a file permission problem. We touch a cache dependency file whenever new pages are created and this should clear the cache, but if folder permissions do not allow modifying files under /Data then it fails to clear the cache.
Make sure the /Data folder and all its children are writable by the web process user.
If files exist at /Data/Sites/1/systemfiles delete them, they should come back on their own if folder permissions are correct.
Hope it helps,
Joe