I have been using Atlas successfully on some folders so I decided to use it on some pages in the root folder of web site. Then I found that pages and web services stopped working in the rest of the web site until I put a bin folder in every sub folder with the Atlas dll in it. This is even if they do not use any Atlas function. I just checked this is also the case with the latest beta. The typical error is "Could not load type 'Microsoft.Web.Services.ScriptModule'" Web services return a long utf error.
I think this has been reported in another post here. Anyone know of an alternative to duplicating bin folders everywhere?