User blog comment:DamiedeterJR/Plothole in A Tale of Two Stans/@comment-27159736-20150716144301

Gideon was more or less just having villainous breakdown when fully seeing journal 3 which result him in hunting Dipper in a frenzied belief that he had the first because he wasn't aware of the amount of journals that were made so he wouldn't have been thinking straight due to dealing with the pines family or bill.

He did believe that Dipper had a journal because he was interorgating him in Little Dipper for how he discovered the crystals so I think he knew about a journal he just wasn't aware of the amount.

you were right about the continued in journal 2 but since journal 3 was damaged or in a bad shape it can presumed that the notice was too damaged to read or he overlooked it.