When you skin a new geometry to the same skeleton, the bind pose often gets trashed. The solution is to delete the bind pose. Select the bind pose node and delete it. Or type delete bindPoseName in the script editor.
Then select the skeleton root and type:
dagPose -save -bp -n "myPose";
This will create a new bind pose. Note that it's not a true bind pose, so that you should actually have the character in the bind pose when you do this. Also note, that it saves the position of all child objects of the skeleton, inlcuding low res geometry eyes and whatnot you might have parented to the joints.
An alternative to writing them down woul be to use the recordPose script, available on highend3d.
Ragnar