If this is B2W2 (U/E), then I'm not sure, personally. Technically, it won't be compatible if any minute details were changed in localisation.
The newer version of PokeCGear actually structures the buttons based on the forest now, so if you are using the higher buttons you need to go deeper into the forest, with the single topmost button being a visually different room. So maybe try putting legendary pokemon only in the glade at the end of the forest?
*update*
Ah, I think I understand now. Certain rooms (depths 3 through 7, and the special depth above 7) are disabled by default.
On a game that has received a pokemon like PGL Arceus, the special depth seems to be unlocked to accommodate it. I don't know much about the forest, so it appears that the total depth can be expanded some way, or unofficially by that long horizontal set of buttons just below your blue box. Prior to this, I had no idea what those buttons did.
[Depth 2] [Depth 3] [Depth 4] [Depth 5] [Depth 6] [Depth 7]
[special depth]