Regarding the garage wall, are you certain it is plastered and not rendered ? The first thought would be that moisture could be coming through the wall from the other (out-?) side. If it is plaster then the prognosis is poorer than if it is render, unless it is plasterboard with a gap behind it.
You certainly can paint over sealant, but the results will depend on the type of sealant. If the sealant is silicone then no paint will remain on it, in the long run no paint will stick to to it. If it is any of a number of types which "bleed" into paint, then the paint will gradually change colour (mostly darken). Acrylic sealant is one that paint will stick to fairly well and not discolour significantly. There is also a sealant called CT-1 which can be overpainted successfully and there are a few others (but not widely used) which have a similar performance. Your description suggests that your example is likely to be silcone, in which case if you want to give your efforts the longest life expectancy you might consider putting on a thin coat of CT-1 over the existing material or even remove the existing and start again.