Hi Dmitry,
I am assuming that the application is running on a Win2003 box. If so, here is one thing you might want to try:
Create a new Application Pool on IIS and associate the ASP.NET 2.0 site with this new Application Pool. Please make shure that sites running on different versions of .NET Framework (1.1 or 2.0) are *NOT* using the same application pool.
HTH.