AVE,
The brakes should work perfectly with DOT 5 fluid. If they don't it is probably the bleeding or adjusting procedure. The experts say that you cannot flush the system and get rid of all the traces of silicone...some will always remain and screw up any attempt to switch to DOT3/4.
These experts also say that if contamination of the system is suspected, you should flush the system a bit periodically with more DOT 5 until it flows clean.
I haven't had a hands on with DOT 5 so this is only 'book learning'...maybe there is a secret way to flush it out.
Having said that, the brakes should still work perfectly with the silicone, unless the system was dirty from DOT 3/4 and things are getting plugged.
Stuart
