What's the difference? Flavour wise, body, fermentability etc.?
Flavor-wise, I don't think there's that much difference, although the unmalted flaked rye might give you more beta-glucans and proteins, possibly giving you problems with cloudiness and poor storage stability if you use too much.
In terms of fermentability, the obvious difference is that malted rye has enough diastatic power to convert itself. If the fancy took you, you could make a beer entirely from malted rye. Flaked rye has zilch for diastatic power, so if you're wanting any conversion, you'll need to mash it with a percentage of base malt which has decent diastatic power.