Darren Duke
Hi if the windows were painted with a top coat of paint it would normally be a gloss paint that would be applied. This is usually an oil based paint and would have a shiny finish. If the finish is matt then its probably just prima undercoat that's been applied. The windows may of been painted prior to the glass being installed. Putty stays soft for ages and can be awkward to paint over when fresh. My advise to you is to start again and apply 2 coats of prima undercoat then a further 2 coats of top coat gloss paint. Use a quality product as cheap products will always be cheap products. Its all about maintenance look after the timber and it will last years, let it slip water gets in, the wood swells, and your back to costly repairs again. I hope this helps? Regards, Darren.