Lumber and Siding - Caulking Stain on clapboards

Hi all, A few years ago a few my father filled in some cuts and gouges in our exterior wood clapboards with latex caulking. He basically filled the cuts and smoothed them out with a putty knife. After priming and painting, soon after the caulked areas began showing a dark stain through the white paint. We have tried more coats of stain kill primer, and more caots of top coat paint but soon the black dirt/mold stain reappears. We are not allowed to power sand our homes where I live and I don't want to replace 20 or so boards on my house. Would something like bondo work to cover over these stains and be painted over? or is there something else I can't think of that I can do? It looks like someone threw a bunch of ash and dirt in some white paint and dabbed it only my house in random spots. Please help. Thanks in advance. dharam

I imagine that you have mold/mildew growth in the caulking that was used. Painting over mold, and the stains caused by mold rarely lasts very long. Even Zinsser's Perma-White, which is "mold proof" suggests 5 years is all they guarantee.

So, you could use the Perma-White and get 5 years out of it... or dig out all the old caulking, scrape and prep the wood, which would involve some sanding (but not necessarily power sanding) and then fill the areas with either bondo or a wood epoxy. Bondo will work well provided the wood isn't getting wet from behind or above. The mold growth makes me suspicious about wetness behind the siding, so you would want to check into that. But at any rate, Bondo won't do well if the wood gets wet, and you can't expect it not to crack on siding joints, since it isn't a glue. In order to achieve the best appearance, you WOULD want to power sand the Bondo, making it smooth with the siding or else the edges of the repairs will make the house look like a patchwork quilt.