Thanks for pictures and info. The sealant you used (2031-205) is manufactured by Momentive (Chemtrec). I verified all the data available and it looks that there is nothing wrong with it, compared with other aquarium safe sealants.
These types of sealant contain silica constituents (or variations). Given that your system is in the third week of life and probably you started to have high amounts of nitrates, then I would say that you have diatoms growing on your sealant. Silica is \"food\" for diatoms and in combination with high nitrates and little bit of light, you got the recipe. Possibly that the silicone grade you used has more available silica and in combination with your aquarium cycle, you got that. Very possible that some diatoms or by-products got into the silicone (diffused into the superficial layer) and coloured the sealant.
Have a look at the following link, scroll down to Brown Algae (diatoms):
http://www.theaquariumwiki.com/Freshwater_algae
I hope this is the cause. In this case you should be OK. Every system is different, and only in certain conditions you have this occurrence.