I really can't say what the difference is flavor-wise. I would suspect little, if any. Flaked rye is unmalted, pre-gelantized add to the mash and it will dissolve quickly. Malted rye is a malted rye kernel, I believe it is huskless. Both need to be mashed and both become quite sticky, so if using even like 10-15% it might not hurt to add rice hulls to mash to prevent a stuck sparge.
I can say it will dry the finish of the beer out. The finish on my rye pale ale reminds of me of the finish of a beer with a decent amount of wheat, only a little different. Sorry for the vagueness, I haven't used rye a whole lot.