what you are saying, if you did all in the right way, it's not your fault, it's because the FR/LG, RNG, while you're in a doungeon, runs faster, it runs at 120 fps instead of 60, but, notice that isn't really the game speed that's increased, it's like that you can hit only ODD or EVEN spreads, like, the game start skipping all even spreads, or all even...
Said so, you can hit only certain ODD or EVEN spreads, so, if you're using Mingot's Tool... make sure that your target Spread has and ODD Frame number, otherwise you'll skip it, since as I said, you'll hit only ODD or EVEN spread, but because mingot tool start counting them as 1 instead of 0, you want to hits ODD ones.
If your target spread is even, all you need to do is to mess up with the game menus, by saving the game, or just entering into the SAVE menu, and then closing it. This will change the kind of spreads that you can hit.
I've the suspect that any menu does that trick, so even just opening and closing, (for example) the pkm menu, should change the kind of spreads that you can hit.