I ran into a problem using Atlas on my page which resulted in a popup showing me an "Unknown Error" alert.
To fix this, try the following: 1. First move all inline javascript on the page into a seperate file. 2. Next, ensure that you are not making any Response.Write(s) to the page. 3. Ensure that you have no HTML tags outside of your documents <html></html> tags. 4. Wrap all update-able controls in an Atlas Update Panel. 5. Finally if non of the above helps and you can afford to take the security risk, add the page directive EnableEventValidation="false".
Good Luck.
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Disclaimer The opinions expressed herein are my own personal opinions and do not represent my employer's view in any way.