Did he say how the timber was treated because even if it gets wet it should resist mould growth. Doesn't sound like your cleaning is to blame it's ridiculous to do more than you are currrently. Wood with has been tanilised (Sp?) is impregnated with a fungicide which inhibits mould growth. As the house gets older it does lose it effectiveness but I'm surprised it's growing mould at 2 months old if it's been treated also your nest box roof is wet, you say, which suggests it's leaking. Is the roof a double pitch or pent and is it felt covered, are there untreated knots which are good water conductors. Treating the wood with a good waterproofer should still do the trick as well as one with an added fungicide.
Stalolan is a clay filler (used in porcellain and paper making) with added disinfecting chemicals chlorine, iron & copper sulfates I believe if my memory serves me right from looking at the website. It's the clay which gives it it's drying properities and in this respect Diatomaceous Earth will be just as effective if not more so, though won't have the useful disinfecting properties. If you have Diatom to hand you could try that or I would think Stalolan is ok for ducks as it is recommended for many farmyard applications with livestock. However you are really treating the symptoms rather than the cause which either must be due to waterproofing or condensation and its preservative treatment. You need to identify the cause and either stop the ingress or improve ventillation as well as give it a coat of water repelant presevative which has also ideally fungicide animal safe properties.
For advice on duck houses you could consult Tory Party Central Office they might know where a second hand duck house is going cheap!
Regards
HF