Hello Alison. Just came across your question while looking for something myself. We had the same problem and eventually came to the conclusion that the brown marks are when water / suds have settled in the folds of the seal and gone off, even a bit mouldy. So the marks on the clothes will be difficult to remove. Just keep treating the marks with a stain remover each time you wash them and occasionally wipe inside the seal to remove the old water. Its a real pain though when you think the machine has ruined your clothes !
Del
June 2009