One of the things you want to check is that you don't have debugging enabled on the server (verify that your <compilation> tag in your web.config file has debug="false").
By default, when debugging is enabled, the Atlas scripts are downloaded on each request. This will slow down your page views.
When debugging is turned off, then the scripts are just downloaded once, and then cached forever on the client. This makes the download sizes of individual page views fairly small.
The symptoms you are describing above sound like debug is set to true.
Hope this helps,
Scott