>They both are 3.5.0 already. However, several other references are 2.0 Should I try to update them?
No, that shouldn't be necessary. Most of the other references haven't been updated to a 3.5-specific version.
Did you upgrade the AjaxControlToolkit as well? If not, that's probably the source of your error.
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>Also why do I need Windows Form in a WEB application?
I've noticed that as well, but I've never had time to investigate it.
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>Do you know how can I copy the references and their versions, BTW? This dialog doesn't seem to allow copy them.
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Sorry, no.