Advanced Skeleton is an incredible suite of character rigging tools for Maya. It is the most comprehensive commercially available toolset that I have seen.
Being that it is so full featured, it once can also run into some issues. As I learn it myself, I am listing some issues and hopefully how to resolve them as I run into them.
FK toe not aligned
This came up after placing joints and building the skeleton. See how to toe and roll circles are misaligned. They should be aligned to one another.
Go back to your joints placement, before building the full skeleton. Select the troublesome joint, then choose freeOrient and add from Advance Skeleton.
Then reorient the joint.
In my case, these settings seemed to work.
Rebuilding your skeleton
I ran into an issue where I needed to rebuild my skeleton from scratch. It can be annoying to have to place all those joints all over again, so I wrote simply python script to help.
#run this part to store joint names and positions of your old advanced skeleton
#obj name and xform
import maya.cmds as cmds
objLs = cmds.ls(sl=True)
for obj in objLs:
objXformLs.append(cmds.xform(obj, query=True, translation=True, worldSpace=True))
#run this part to load those positions onto a fresh advanced skeleton
for index, obj in enumerate(objNameLs):
print index, item
cmds.xform(obj, ws=1, t=(objXformLs[index],objXformLs[index],objXformLs[index]))