Interesting thread. It mentions both pathological and non pathological causes of black spots. OP, how are your clowns now and did you read through the thread M Morti shared?There is an old thread here with a few ideas
Mysterious black spots on clown loach
I was looking at my two clown loaches thee about 7-8 cm in length and the only other diesieses they have had is ich but that was a couple month ago ,they are well fed too ,but anyways they are more like black sploches and there over lapping each other,some are dark and some are light but there...www.monsterfishkeepers.com