I created an Avastar avatar using a shape XML file exported from Second Life.
The yellow IK bones are used to position hands and feet. When I save the file, and then either close and reopen it again, or select File => Revert, I find the IK bone position and rotation edits were not saved. How is the IK bone position and rotation data saved with the rest of the file?
You do add keyframes for them? If you do, most probably the actual controls are some other bones/objects and bones you are posing are not the ones that need keyframing. Does the animation play back as it should of you animate them and scrub the timeline?