On further testing, with Open in Tabs off, if I open a script when Script Debugger is not already running, the cursor always goes to the bottom of the window. If Script Debugger is already running, the cursor is where it was when the file was saved.
Seems like something Mark should check out at some point.
Either way, the window always opens scrolled down as far as it can be without the cursor being hidden beyond the top of the window. So for example, with the cursor at line 20 in a 200 line script, the window scrolls on opening so the cursor is at the top of the window. A bit hard to describe, and I'm not sure if that's the intended behaviour.