If you use isopropanol, the version that's more pure works better. Standard rubbing alcohol is 70% I think, but you can buy 90%. The main thing is to NOT breathe the vapors, but this is usually not a problem because they smell weird anyway. The trick when cooking is to cover any pots or metal cups with a good lid. Otherwise some of the alcohol vapor can condense on cooler surfaces and drip down into your food or drink.
Pete,
Obviously the 90% stuff will have higher heat content, but isn't it a sooty, nasty mess when you burn it? The 70% stuff burns cleaner, yes?
What kind of a stove were you burning it on? Do you have any photos of your set up?
HJ