Question : VS 2003 with .NET Framework 3.5

I am working on an application which was developed on Visual Studio 2003 and .NET Framework 1.1. Recently the server has been updated and it ow has .NET Framework 3.5.
The application is working but with lots of issues like windows closing down suddenly, search boxes not working, pop ups not working etc.
Is is because .NET Framework does not go well with VS 2003?
If yes, then should .NET framework be down graded to Framework 1.1?
Or will upgrading to VS 2008 work ?

Answer : VS 2003 with .NET Framework 3.5

You can have many versions of .NET Framework loaded on a server.  Even if you have 3.5 on your server, you can still install and run applications with the 1.1 Framework.  

Check the appPool setting for your web site and make sure the correct Framework version is selected for your website (although the web configuration should specify the correct version anyway).