I am not sure how you have created this part. When you add pins and you place them to touch the body of the symbols, they will be positioned just as you see them on the screen. I suggest you re-creating this part using CAE Decal Wizard.
I used the CAE Decal Wizard. Each time I create the part, the pin numbers do not line up with the actual pins. They are off by 3.
If I go thru the PADS Logic Tutorial, Creating a CAE Decal with the CAE Decal WIzard, as soon as the decal is created, the pins and names are always off by 3.
The pin decal is defined in one of your libraries. The pin number location is defined in that library. I'm not sure why you seem to have a non-standard decal. Logic searches the Library List from top to bottom, so if there are copies of the pin decal in multiple libraries it will use the first one it finds.
To find the pin decal, pull up 'Library Manager', set your library selection to 'all libraries', set your filter to Logic, and your search criteria to "PIN*" and press apply. Then double click on a pin definition to reduce the search to a single library and the 'edit' button will no longer be grayed-out.