Regarding the main issue "Multiple controls with the same ID 'ScriptManager' were found":

• do you have ajax.net installed?
• do you use special JS scripts in your skin?

This happens across many very different skins on my instance, most if not all without any additional script.

I do have a generic PNG Fix script in my default.aspx,  and I have the following in my httphandlers section for ajax:

      <!-- ASP.NET AJAX support -->
      <remove verb="*" path="*.asmx" />
      <add verb="*" path="*.asmx" validate="false" type="System.Web.Script.Services.ScriptHandlerFactory, System.Web.Extensions, Version=1.0.61025.0, Culture=neutral, PublicKeyToken=31bf3856ad364e35" />
      <add verb="*" path="*_AppService.axd" validate="false" type="System.Web.Script.Services.ScriptHandlerFactory, System.Web.Extensions, Version=1.0.61025.0, Culture=neutral, PublicKeyToken=31bf3856ad364e35" />
      <add verb="GET,HEAD" path="ScriptResource.axd" type="System.Web.Handlers.ScriptResourceHandler, System.Web.Extensions, Version=1.0.61025.0, Culture=neutral, PublicKeyToken=31bf3856ad364e35" validate="false" />
      <add verb="POST,GET" path="ajaxpro/*.ashx" type="AjaxPro.AjaxHandlerFactory, AjaxPro.2" />

The ajaxpro bit is installed by Bizmodules' Ultra Media Gallery.