I strongly doubt that it was intentionally done by Nintendo -- even if it is a glitch, although I also have some doubts about that. Other people have managed to find all the Poes just fine, and I don't think they'd make it so that SOME games do not work and others play just fine. Like I said, for that reason, I even find it hard to believe that it's a glitch, but I believe that you looked over every area again. I've had thoughts sometimes that the reason I can't find the last Heart Piece in A Link to the Past must be because of a glitch too, since I also checked back over every single place again, but I know how unlikely that is.
Haha, or is there an overabundance of people who've gone through the same process as you? You said you found lots of threads detailing the same problem, so I guess I could be wrong.
I feel really sorry for you, because like I said, something very similar happened to me in A Link to the Past, and it was EXTREMELY frustrating. It's so terrible to know that you worked so hard and yet you still can't call the game 100%. I'd suggest leaving the game for a while -- probably a few months -- and then going and rechecking everywhere again. Maybe that'll help? It might give you a new outlook, so that you're not constantly thinking, even subconsciously, "I already checked this place, so I don't need to check it as thoroughly this time..."
I have to say, though, it's an incredible feat that you managed to collect 59 of them in the first place. I never got even close to that -- I think I was somewhere around 35, maybe 40-something. The fact that there is no way to change day into night just made that entire quest immensely tedious for me. I didn't want to have to wait around for nighttime to go and do a sidequest. Not to mention that days last way longer in that game than in something like Ocarina of Time.