The file upload worked for me before I changed anything... but I did update the page page_content_update.php to use the new editor from the beta to see if you prefer it.
I did notice that the original file list in the old editor actually shows the wrong folder content.
To update your other pages to use the new file manager, just find the line that begins with:
$CKEditor_config["filebrowserBrowseUrl"]
and then update it to match the one that I have already changed.