As mentioned in the comments, you're probably getting the same key for both registrations. Try this way:
Page currentPage = (Page)HttpContext.Current.Handler;
ScriptManager.RegisterStartupScript(currentPage, typeof(string),
"Script" + Guid.NewGuid, "alert('1!');", true);
ScriptManager.RegisterStartupScript(currentPage, typeof(string),
"Script" + Guid.NewGuid, "alert('2!');", true);
Or merge both scripts into a single one and make just one registration.