Well, about the ASP.NET 2.0 i got it fixed.
I just created two different application pools, one for applications using .NET 1.1.4 and another one for applications using .NET 2.0.
Running on different process, the applications works just fine, no more craches.
Now, i believe that, to integrate it with my portal i need some documentation but the help file (CuteChatdeveloperguide.chm) doesn't work on my pc.
I can open it and see the table of contents but nothing is displayed on the right side, just a blank screen for all topics.