I have an asp:UpdatePanel with an asp:Timer. These are in a Master/Content Page. The code is below:
Is there a specifc reason why you have the Timer control in the UpdatePanel?
Every time I have needed to use a Timer control to cause an UpdatePanel refresh, I have set it up like the following and it works fine with MasterPages:
Use the Trigger to cause the UpdatePanel to refresh from the Tick event. You only want to embed content in your UpdatePanel if possible.