I just finished my lengthy SS playthrough (due to dropping in and out of it, finishing New Vegas and starting DN Forever).
I doubt the difficulty affects it, I played this on my other account on Normal until just after learning about Stealth Kills. Then I changed to my main account and went straight on Supersoldier. Though like another poster my connection died near the end of the game. When I finished it I got all the difficulty achievements.
I don't think there's any logic to this glitch, either you get it or you don't and even a recent patch doesn't seem to have fixed it by what I've read here.