I have the same problem. At first I was happy the AutocompleteExtender in the Toolkit would stop the message with the "secure and non-secure items", which appeared using SSL previously.
Now I don't have this issue anymore, but the problem with the two ids. Actually it's annoying to falling from one problem to the other with every "release"...

My code and settings are as following:
-Using Master Pages
-Using AutocompleteExtender within ascx user control
-within user control is a scriptmanagerproxy
-the I have an UpdatePanel containing the textbox and extender

<asp:TextBox ID="txtLocations" runat="server" AutoCompleteType="Disabled"></asp:TextBox>
<ajax:AutoCompleteExtender ID="aceLocations" runat="server" MinimumPrefixLength="2"
 ServiceMethod="GetLocationList" ServicePath="~/WebServices/Service.asmx"
 TargetControlID="txtLocations" CompletionInterval="500"
 EnableCaching="true"/>

-the application is set to debug=true
-the website is running iis 6.0 locally (not asp development server)
-site is allowed to be updateable (this setting is historic since the rc1 release had a major problem with "release" compilation)

Any help appreciated,

Chris