Eric,
I'm afraid you are expecting a little to much. If you exclude the parent group for the annotation then the layers under it will not be able to toggle. If you try and remove just the specific anno layers and have then still controlled by the parent layer this is just not going to happen.
Unfortunately no it is not. So where is the command line telling the XML where to look for the TOC elements? As you can tell I am new to this, but following other layer codes, there is a line that designates a particular layer if needed. Is this widget different.
Do you have a suggestion for learning the basics of working FlexBuilder 4.3?
John,
If your map services are not publicly accessible than you are just plain out of luck and it is time to upgrade.