It's best to control the animated object either all on the timeline or all in code when it comes to interpolation and appearance, due to how the player works (it takes over). If you do the color transform in the PI (or the animation in runtime) you should be OK.
10x for your response.
But after i create one more aditional movie clips all animation becomes invisible but first frame color transformed correctly.
Is there one more place where should i do transformation?
Would you be so kind as to list all places where should i do transformation without animation loss?
It depends on whether you want to do code or not. You can do color transforms in the PI (select the instance and add it in the Color Effect section, remove or comment out the transform code), or if you prefer to do everything using code then try animating the IK using code instead and remove the timeline animation (http://help.adobe.com/en_US/AS3LCR/Flash_10.0/fl/ik/package-detail.html).
The problem is: when i add filter or transform in code or timeline to shapeBone1 the bone becomes static and stops animation.
I get it. I should wrap inner of shaepeBone1 with MovieClip and everything woks fine.
Question: Why i should do this?
This is not normal UNDOCUMENTED behavior. So this is bug.
I understand the behavior (in relation to other cases like this), and it's actually expected (by the Flash Player). It was an intentional change made after Flash Player 8. I'm not sure if documentation or tech notes have it covered somewhere but similar cases have been covered online.