Ok, I finally caught my Palkia but something really strange happened. I kept hitting weird frames until I began seeing I was hitting an even frame, meaning that the -5 I was applying was wrong. So I cut it to -4 and voila, I began hitting a Calm Palkia who was at least at an odd frame. Found out that such Palkia was actually at frame 91, one more journal flip from what I did the first time I hit my seed, flipped the journal 40 times and walked 128 steps. It was "impossible" for I had counted one by one (at this point, I was being very cautious about the flips plus with 40 I knew where it had to end since I was going back and forth). So, after hitting my seed for the 14th time, I decide to only flip the journal 39 times and walk the 128 steps, still using the -4 modifier instead of the -5 I should really have. Boom, the 31/31/31/31/31/31 Palkia appeared.
It was bound to happen and finally I caught my Palkia, but my question still remains for future legendary RNG'ing: How did that modifier became -4 instead of -5? Where did I advance those extra two frames? I know the second question can be answered by saying: Well, you screwed up by one, no biggie. I know this is not the answer for multiple reasons, but most importantly: When you are going back and forth between two journal pages you know which one is the "odd" number page and which one is the "even" number page. In my case, the first was a caught Dialga page and the second a defeated Roselia page. In the attempt where I landed in the 91st frame, the journal ended open at the even page or the Roselia page. In my latest attempt, the last page opened was the Dialga page.
"Well, you went through another caught/defeated page without noticing". Problem is. Besides the "Started at spear pillar page", the only page before the Dialga page was this one:
"Jun. 3 Thursday
Started from Oreburgh City.
Used Strength at Mt. Coronet.
Used Rock Climb at Mt. Coronet.
Got through Mt. Coronet.
Used Rock Climb at Mt. Coronet"
So where did those changes come from? Even if I caught the Palkia I'd still like to know to keep it in mind once I begin RNG'ing the birds.