doc.pageItems...

can lead 'into' the wrong document - so 'doc' is OK, but 'doc.pageItems.item(0)' is wrong.

Observe this script, which uses doc.pageItems (InDesign collections) as well as doc.labeledPageItems (APID hack). doc.labeledPageItems always picks up the correct page items (but of course, it's an inefficient way to find the page items), whereas doc.pageItems (with the _same_ doc) goes wrong depending on which of the two same-name docs is the active document.

var doc = app.activeDocument;

doc.pageItems.item(0).fillColor="C=100 M=0 Y=0 K=0";
doc.pageItems.item(1).fillColor="C=0 M=100 Y=0 K=0";

var pageItems = GetPageItems(doc);
pageItems[0].fillColor="Black";
pageItems[1].fillColor="C=0 M=0 Y=100 K=0";

function GetPageItems(doc)
{
     var allPageItems = doc.labeledPageItems("*");
     var retVal = [];
     for (var idx = 0; idx < allPageItems.length; idx++)
     {
           var item = allPageItems[idx];
           if (item.parent instanceof Page || item.parent instanceof Spread)
           {
                 retVal.push(item);
           }
     }

  return retVal;
}

I _could_ write some solution, but the problem runs deep, and the task would be fairly daunting - I would need to replace the whole collection mechanism inside InDesign. Even things like doc.swatches... go wrong (that's why I am using named swatches).

Another indication to how bad it is - even the debugger is confused and shows the wrong document contents in the browser, while the effect of pageItems[0].fillColor="Black"; clearly shows that doc is correct.

Bad 'un.