GBA pokemon hacking is a pain but there are extensive tools available to you.
A good start is
http://www.romhacking.net/utils/463/ and
http://www.romhacking.net/utils/427/ might also be of interest. There are a few forums like
http://www.pokecommunity.com/ that used to have a great hacking section but since went "private" so I have no idea where they are at these days.
Your AV program may have issues- it packs more programs into itself (a common virus behaviour) but it is good.
http://donnus.tripod.com/maker.html might also be worth a little look in for various things.