Why is the theft system light &/or battery light coming on when I start car?

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Sometimes when I start my car the theft system light and/or battery light comes on & I can't roll down/up windows, turn on air & gear light doen't come on. After a few minutes something in the engine makes a noise and they go off & I can roll down/up windows etc. I tried unplugging battery & it didn't reset. My anti-lock light & brake light came on close to a year ago & my fathers mechanic said anti-lock brake part went bad (has not been replaced). I'm not sure if that could have started this theft/battery light problem. Not to mention intake manifold is leaking coolant.