Thanks for reporting this @joh13213 - the scrolling change was not intentional, and we are looking into it. And thanks to @Mark_Bailey for the workaround - it seems to work well to embed the <<ScrollWindow message directly into the New Window() call:
dt=Open("$SAMPLE_DATA/Big Class.jmp");
New Window("test",
dt << Run Script("Bivariate"),
dt << Run Script("Oneway"),
dt << Run Script("Distribution"),
<<Scroll Window(0,0)
);