Firstly, and maybe it's because I haven't met the mythical "bone tool user"
but I haven't used it, and none of the other people that I know working professionally bother with it.
This might be due to being older and less familiar with it... but let me just suggest:
don't use the bone tool in flash.
If I remember correctly, it actually forces you to turn all of your component parts into MC's so that's probably the problem your running into. There are good 2d ik tools out there, but not the one that comes with flash. From what I understand ToonBoom has a pretty good rig set up, so if your heart is set on it, I think Toonboom has a freeware version or a pretty cheap learning version.