When I look at my perk chart, I have 5 stars in perception, 7 in agility. But on my attributes screen, my perception is (-) 2, agility (-) 5. The sad part? It had been like this for well over 50 hours, and I always disregarded it thinking it was because I carry a heavy load at all times (150lb+). I finally decided to take everything off when I was moving junk from one base to another, and I realized the stats were still the same. Debuff bug. So all this time I've been playing Survival+ with gimped stats. I always wondered why I can only get 2 sniper shots off in VATS, and why my accuracy svcks at range.
I have no idea what caused this, so I'm not even going to bother to reroll. At times when I felt the game was being difficult, I simply adapted and adjusted my style, never once thinking that I was bugged. You guys think the molerat disease -10hp is annoying? This is ten times worse. No I have never noticed any abnormalities, like blurred vision (head cripple bug), I even tried crippling my head or limbs by blowing myself up with a grenade and then healing again, no difference. I have never used the console except for one time, to advance the quest stage for Emogene's bugged quest. Never did plastic surgery, never altered my character in any way.
If anyone can shed some light on this, that would be great, but I"m not holding out much hope, and I don't think even a patch can fix a bugged save. So let this be a warning to all of you, always check your S.P.E.C.I.A.L. stats from time to time especially after suffering an injury, and make sure you fully heal yourself up before making a backup save.