I did have a similar thing (not exactly half the size tho). When choosing 'New' doc in Painter by mistake I'd changed the Resolution from pixels per inch, to pixels per CM. Don't know if that's your prob, but make sure it's pixels per inch.

To check it on an already created doc, go to Canvas/Resize and if it's pixels per CM change it.....you then may have to alter the size.

Not sure about the flattened bit tho. If you had layers they should remain as layers.