I am having what I believe should be a fairly simple problem, but for the life of me I cannot see my problem. The problem is related to ScriptManager.RegisterStartupScript,
What worked for me, is registering it on the Page while specifying the type as that of the UpdatePanel, like so:
ScriptManager.RegisterClientScriptBlock(this.Page, typeof(UpdatePanel) Guid.NewGuid().ToString(), myScript, true);