I think I would use the word stupid for me rather than brave.
I updated through the Sony site and have the updated 1.04 version.
Root package still there.
I then did the suggestion of a couple of posts up and tried to remove the root. No luck.
Perhaps I should explain what I did to make sure I am doing it correctly.
I clicked on the link, downloaded to my computer, connected my reader to my computer, did data transfer. Reader shows up on my computer. I take the restore file and place it into the reader drive, click flash-bat...type Y and let it do it's stuff. Reader powers down and then reboots. Root still there.
Next?