IPad 2 Safari javascript window.open bug

I am building a web app that uses the PicUp app to upload photos.
Part of how it works requires me to open a new tab with javascript, which fires some script to open a new url in an iframe on the previous page.
I have named the 'windows' accordingly, and it works properly on the iPad 1 (Safari).
But in iPad 2, the window.open function does not seem to take in a target window parameter, resulting in broken UI. The new tab opens, but the script to open a new URL in the other page's iframe does not work.
My image still uploads, but the user would be confused, as there is no confirmation screen.
Help!
PS: I would also like to comment that it is fairly convoluted to have to download a 3rd party app just to handle http uploads, something every other browser can do natively. What is the reasoning behind not allowing iOS Safari to upload like normal?
Thanks
John

Was able to produce a small test case. 
To demonstrate this problem, there are three pages.  You will need to load window1.html.  That page has buttons to load the other windows.  Make sure all files are in the same directory.
window1.html
<html>
<head></head>
<body>
<script>
window.name='win1';
var si = setInterval('check()', 1000);
function check()
    var d = new Date();
    var s = d.toString() + ' hash: ' + window.location.hash + "\n";
    var log = document.getElementById('log');
    log.value += s;
    log.scrollTop = log.scrollHeight
</script>
<form name='myform'>
<input type=button name='cmd' value='Start second window (no close)' onclick="window.open('window2.html', 'win2')">  
<input type=button name='cmd' value='Start third window (with close)' onclick="window.open('window3.html', 'win2')">
<br />
<textarea cols=80 rows=10 id='log'></textarea>
</form>
</body>
</html>
window2.html
<html>
<head></head>
<body>
<script>
window.open('window1.html#from2','win1');
</script>
<p>This is window2.html</p>
</body>
</html>
window3.html
<html>
<head></head>
<body>
<script>
window.open('window1.html#from3','win1');
window.close();
</script>
<p>This is window3.html</p>
</body>
</html>
Test scenario:
If you run window1.html, you will see it is updating the text field with the time and displaying the current hash.  If you press the button 'Start second window (no close)', you will see another tab open up and stay there and the window1 text field will display the hash 'from2'.
You can close the window2 tab if you want now (don't think it matters).
If you then press the button 'Start third window (with close), the window1 tab is gone and window3 is still up there.  The title bar says it is window3 but it is not even displaying 'This is window3.html'  If I do a view source (using a javascript bookmark), it does show the window3 script but the <p> and text is not there.  Probably died in the script before parsing was finished.  This is the first problem.
Now load the window1.html again in the browser (type on URL line).  If you press the 'Start second window (no close)", the one that worked before, and click on the window1 tab to view it and display the updating text box, you will see it did not see the hash change.  This looks like that physical tab was corrupted in Safari from the window 3 test.  I just found if you open a new tab, the new tab will be ok to run the second window (no close test).  At least until you run window3 (with the close).

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