Hard to say without seeing the problem but such problems are usually caused by either condensation or trapped moisture.
It could be that your old windows were a bit drafty but were also providing adequate ventilation to prevent the build-up of condensation in this area.
Or, they have used a hard, non-breathable damp-proofing plaster and/or paint finish which is holding in moisture behind the surface. This could cause a cold-spot which is allowing moisture in the air to condense on the surface - hence the black mould. This would also explain why paint is flaking-off because the trapped moisture is forcing its way out.
As I say, pure guesswork on my part, but you will need to get to the root of the problem before attempting to redecorate.