I think I figured it out. It is quite obvious actually. I have many Dittos so I am usually able to use the natured Ditto I want/need. For instance...if I wanted an Adamant Azumarill then I would use a random natured male marill/Azumarill to breed with an Adamant Ditto with Everstone. So it increased the chance that I would get Adamant. Where as I think other people might have used the Everstone and a nature they didn't want such as a Modest natured Ditto. I can totally see how this could mess up the RNG because the RNG assumes that nothing is messing with the nature...to change it anyways. Where as, the Everstone would only increase the chance that I could get Adamant in my case it would drastically decrease the chance in the other.As Bakus had said, if the everstone thing seems to work for you, I guess just go with it.
I don't know how to help you fix your problem, as I can't see what you're doing or what's really going on. All I can really suggest is keep using the everstone I suppose. Since it seems to be working amazingly well for you.
Sorry I couldn't have been of better help,
~Zombie.
I still don't know why it messed up for me before but I attempted getting a Hasty Houndour yesterday, without an Everstone on my Naive Ditto and it worked this time. So, I guess I am ok now...lol.