Trainer Levels are Insanely high for the start of randomizer

[IHaveQuestions]

I just started a new randomizer and I noticed my rival and other trainers were almost double the level the should be, So I go back into pk3DS and look to see that there is a option to make the trainers Pokemon 50% higher leveled. So I re-randomize it with the option off, but still, their Pokemon are still high level. So then I download the newest version and try again, Roxanne has level 27 and 31 Pokemon when they should be levels 12 and 14. Is there any fix to this? Any help is appreciated. Also I'm new to this site so I apologize if I shouldn't had made a new topic. 

'mm new to the site so I'm 

[Ruby Genseki]

I'm assuming you re-randomized the same ROM, where the trainers' Mons were already overleveled. If that's they'll remain that way because that'd be what the tool now recognizes as their "original" level, therefore leaving it as is.
Try randomizing an unedited game, making sure that setting is off from the start.