I’ve set my texture size to 4096x4096. I go into Tool > Texture Map and either select this texture or press the New Txtr button, then the New from Polypaint button. Everything looks good except that the texture is 2048x2048??! It has completely ignored the 4096x4096 texture and size I set in the usual texture palette settings. Is polypaint limited to a 2048 texture or something? 
In 3.5 you need to set the Texture size in the Tool>UV Map submenu.
Yep that did it! cheers Marcus 