All depends of what you wanna do exactly, as you probably know JK2/JKA anims are directly "coded in",you just apply the base JK2 or JKA skeleton to your models, and then it will run correctly(this works of course, since you just put a bip,it's the same for quake3).
But there is a slight difference with JK2/JKA, if for example,you have a character that you got to work in JK2, with the standard JK2 skeleton(not with custom anims), then you'll see that the model works perfectly in JKA as well.They used the same skeleton for JK2 and JKA, and the engine adapt the animations to the model directly,so when you use a JK2 model(so exported,in a pk3 etc,like a normal model), the engine will itself put JKA anims on it.
So if you have a JK2 model with the standard JK2 skeleton, just put the model(pk3) in your JKA directory,and you'll see by yourself that the model works perfectly and that the model has JKA anims and not JK2 anims.
I didn't try it with the Standard JK2 models though, i made a few models and exported them to JK2,and then tried them in JKA and they worked perfectly. It's weird that you have some bugs in JKA that aren't here in JK2
I hope that i've been able to help you
BTw : Hello to everybody, just signed in here =)