I went digging and I found a save file of my perfect timid HG spread in another folder. It was before Red, before unlocking latias. So I unlocked latias and did the necessary steps to get to the Elite 4 to RNG it. I also made sure I had the enigma stone event on a Wondercard, to make this file as close to the same as the other file, so that only Red was different. I ended up with the same wild delays that leapt upward by increments of 50 or so. This was with Red still on his mountain. I haven't even unlocked the area. So that rules out Red on my game.
For me this leaves two possibilities: 1) The enigma stone, which I can rule out by doing the same steps again on a file where I do not receive the wondercard, and 2) the order in which I do the roamers, latias being last somehow causes weirdness when I haven't fainted them in order (this second option doesn't see so likely to me because I'm sure many people went after latias first since it's in a higher class).
For me this leaves two possibilities: 1) The enigma stone, which I can rule out by doing the same steps again on a file where I do not receive the wondercard, and 2) the order in which I do the roamers, latias being last somehow causes weirdness when I haven't fainted them in order (this second option doesn't see so likely to me because I'm sure many people went after latias first since it's in a higher class).