O well, I believe this is specific to Jabo's plugin in 1964. 1964 does not support the resize. PJ has a new ini setting for just this. In the meantime you can use Jabo 1.3.
... as a workaround copy the pj64 ini ("rdb") into your 1964 folder. Jabo's fetches the parameter from this particular file only and the emu isn't involved at all. Dirty, but it works
edit: guess this should work for the Euro thingie as well, only tried it with Conker US and it seemed to work
BTW anyone know how to fix the letter box prob (JFG)???