I thought brown diatoms were caused by high silicates. ??
When mine didn't appear be getting any better and in fact seemed to be getting worse even after 3-4 months I finally added PhosZorb to my filter. It made a noticeable difference rather quickly. After several weeks they were gone. I don't know if it was just a coincidence they cleared up when I added the PhosZorb or not, but when they started again after changing my substrate I put the bags back in and they started going away. Again could have been coincidence. But to me it seemed to help. I dose extra Phosphate to put back in what is removed.