The colour comes from the brand & type of synthetic oil used in the mixture - methanol and nitromethane are clear and castor oil (if you're using it) is a light brownish colour. Generally it won't make much difference what oil's in the fuel (as long as it's an oil meant for glow engines of course!). Using more nitro than the engine requires will rob a little power, as will too little but again that's not a significant difference. Fuel can "go bad" if it's left open to the atmosphere too long, especially in humid weather as it absorbs moisture from the air. There's no visual way of telling if it's absorbed moisture, and as far as I know there's no way of removing it either.

If the engine's playing up on the ground and getting worse in the air chances are it's running lean (either on high or low speed needles, or both). This is bad for several reasons... it makes your plane crash, and the engine overheats (running lean = running hot) and doesn't have enough lubricant.