So, about 12 hours into my play-through the first rank of the sniper perk decided to stop working, or, at least half of it. I can still seem to hold my breath as long, but the stability boost refuses to work at all.
This happened abruptly, and i noticed right away because with two stabilized arm mods and the perk bonus, there's practically no noticeable sway with any scoped rifle while you're crouched. I tested the possibility that the glitch was to do with the armor or weapon mods, but to no avail.
I reloaded an older (about a day) save and was able to continue for a while, but sure enough at around the same playtime it cut out again. This time I had an auto-save right before it happened, and was able to play around with it a bit. It was strange, I scope in and it's working, so i scope out and immediately scope back in, and it's not working. One second good, the next broken.
The two times it happened were at two different locations and times of the day (outside vault 95 at night, and in Diamond City at mid-day respectively), and there was no apparent link to any quests. I only had Dogmeat as a companion, and didn't take any new perks close to either time.
15 hours into the same character and it hasn't come right on it's own. The perk was always a little buggy, you'd sometimes have to wait about a second after scoping in for the cross-hair to stabilize, but it's pretty annoying for it to stop working entirely, particularly since this is such a useful perk.
That said, to play for this long in a game this big and only encounter something of this caliber, that's not doing too bad. Fallout 4 is still the best game I've ever played, and this is hardly a game-breaking bug, but it would still be pretty cool if this got fixed, as I'm sure it will eventually