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This is what happened.A few years ago I replaced all brake parts from master cylinder to calipers.Filled with silicone brake fluid.A few days ago, I replaced the master cylinder again,this time I used dot 3 fluid.I used a pressure bleeder and ran about a gallon through the system to flush out the silicone fluid.I rebleed the system about 2 weeks later(I didn't even drive the car in between times)the fluid had a blackish color to it.All wheels had this color.I would flush it out till it ran clear into a glass jar.When I would go to the next wheel(with the clear fluid in the jar) It looked really black.What's happened?? :cry
Silicon and DOT 3 are not compatible. You need to flush the system with alcohol if you're changing from one to the other.
Generally speaking, when you see black in the brake fluid it's from dissolved rubber from the seals in the brake system. I don't know whether the silicon/DOT combination will dissove rubber or not; I've never done that myself. Could be the combination isn't good for the rubber components and is causing them to dissove into the mixture.
If it were mine, I'd go back and flush the system with alcohol and replace with your fluid of choice, and hope for the best.