This thread on the Adobe forums community has the following JSX script to help with this issue (it changes the global preferences of the ruler origin so that it uses the first quadrant again instead of the fourth)
#target Illustrator
// script.name = switchRulerOriginToCS4nCS5.jsx;
// script.description = switches ruler origin to bottom/left (like CS4), and back to top/left (like CS5);
// script.required = runs on CS5 only;
// script.parent = carlos canto // 8/12/11;
// script.elegant = false;
var appver = Number(String(app.version).split(".")[0]);
if (appver >= 15)
{
//var idoc = app.activeDocument;
var win = new Window("dialog","Set Coordinate System");
var grpCoordinates = win.add("group");
var grpCS4 = grpCoordinates.add("group");
var lblCS4dummy = grpCS4.add("statictext",undefined,"CS4");
var panely1 = grpCS4.add("panel");
var lblCS4 = grpCS4.add("statictext",undefined,"CS4");
var panelx = grpCoordinates.add("panel");
var grpCS5 = grpCoordinates.add("group");
var lblCS5dummy = grpCS5.add("statictext",undefined,"CS5");
var panely2 = grpCS5.add("panel");
var lblCS5 = grpCS5.add("statictext",undefined,"CS5");
grpCoordinates.orientation = "column";
lblCS4dummy.visible = lblCS5dummy.visible = false;
var panelradio = win.add("panel", undefined, "Ruler Origin as in...");
panely1.bounds = {x:0, y:0, width:0, height:60};
panelx.bounds = {x:0, y:0, width:120, height:0};
panely2.bounds = {x:0, y:0, width:0, height:60};
grpCoordinates.spacing = 0;
win.helpTip = grpCoordinates.helpTip = "Double-Click where the rulers meet to update \rCurrent Doc's Ruler Origin...";
grpCoordinates.helpTip = "Coded by CarlosCanto";
grpCS4.helpTip = "CS4: Positive Y moving up";
grpCS5.helpTip = "CS5: Positive Y moving down";
lblCS4.helpTip = lblCS5.helpTip = "Don't click me...";
//add Radio buttons
var grpRadio = panelradio.add("group");
var radCS4 = grpRadio.add("radiobutton",undefined,"CS4");
var radCS5 = grpRadio.add("radiobutton",undefined,"CS5");
var btnOk = grpRadio.add("button", undefined, "Ok");
btnOk.size = [40,25];
btnOk.enabled = false;
//radCenter.value = true;
win.defaultElement = lblCS4dummy; // make this element default to prevent hitting "enter" to trigger ok button
radCS4.onClick = function(){
// alert(idoc.name);
lblCS4.visible = true;
lblCS5.visible = false;
btnOk.enabled = true;
}
radCS5.onClick = function(){
//alert(idoc.name);
lblCS4.visible = false;
lblCS5.visible = true;
btnOk.enabled = true;
}
btnOk.onClick = function(){
//alert(radCS5.value);
app.preferences.setBooleanPreference ("isRulerOriginTopLeft",radCS5.value);
app.preferences.setBooleanPreference ("isRulerIn4thQuad",radCS5.value);
win.close();
}
lblCS4.onClick = lblCS5.onClick = function(){
alert("...we're so damn curious, aren't we?");
}
win.center();
win.show();
}
else
{
alert("CS4 and earlier don't need this trick...good bye.")
}
Source: http://forums.adobe.com/message/3859266#3859266