I use flaked rye quite often and have never have a problem.
I also did a rye bread ipa today. Along with flaked rye, I used 1.25 pounds of rye bread as an experiment in the mash. To further that experiment, I took off 8 cups of first runnings and decocted (down to 2 cups) it along with another 1.25 pounds of rye bread. It was a stick mess but appears to have worked out.
I did this based on the flavor of the local bakeries rye bread and wanting to see how it worked in a beer.
If it doesn't work out, lesson learned but if it does work out, I might have made a winner.