Any suggestion for these situation?
So what I did to get around the error was I made a small change to the runtime.js. On line 161 I changed:
inst.instance_vars = save_obj["inst_vars"].slice();
to
while(inst.instance_vars.length > save_obj["inst_vars"].length)
save_obj["inst_vars"].push(0)
inst.instance_vars = save_obj["inst_vars"].slice();
It means if you have any instance variables set through the IDE (that spritebank does not know about) they will be reset to 0, but it at least lets you load the spritebank so you can resave the json.
I guess this doesn't solve the problem posed by you if you are updating instance variables through the IDE. That I'm not sure of, I think I need to learn more about how plugins work <img src="smileys/smiley1.gif" border="0" align="middle" />