Glad you got us back into the issue about the spots just on the sealent.
I found that before I started useing Dicor sealent and just used silicone that I had spots too.
I think it is mold actually under the layers of sealent so washing on outside skin of the silcone.
I took as much of the sealent off with a razor blade and reapplied with Dicor
Fiberglass Roof Coating, applied, from can, with fingers and posicle stick.
2 years and no staining under applications as of yet.
Keeping fingers crossed in Maine.