This bug has been fixed for Maya 2013.
There seems to be a bug with either the ik solver or the ik handles in Maya 2012 when loading a scene. Recently I noticed that a rig from two different scenes of two different projects, set up in Maya 2012, wouldn’t move as expected when the scene is opened again. I.e. moving a characters leg with the foot control in ik mode would move the foot but the leg would stay behind.
A workaround for this problem is to update the evaluation of the ik solver through the menu in Modify/Evaluate Nodes/Evaluate All.
Unfortunately this has to be done every time the scene gets loaded, so I was looking for a way to do that automatically during every loading of a scene. One of the scripts that usually gets evaluated during scene load is “selectionMaskResetAll” found in “selectionMaskStackInit.mel” in the “scripts/startup” directory of the Maya.
In there I added
doEnableNodeItems true all;
which does the same as the “Evaluate All” item and now the scenes load fine.
You can download the modified script here: selectionMaskStackInit.mel
Place it in one of the user script directories that Maya will scan during startup. This way the original script stays in place (just for safety reasons) but the copy will still get evaluated after all scripts in the application folder.