Try reflashing it again, but then open MegaTune, connect to the box, and DO NOT load values.
Save the MSQ and with the box CONNECTED and POWERED ON edit the values. Again, don't load an MSQ, edit them by hand (each thing one by one like on the sticky).
When it doesn't hold values like this it is usually caused by corruption when you load an MSQ on a box that's never really been configured.
Once you have typed everything and burned them, cycle power to the box and double check that nothing changed. Once you do this once then you'll be able to edit values with the box disconnected and burn them by connecting it and loading the MSQ.
Mario