Originally Posted by NAIMA
this just messes up the skin tough ....
You're not exiting the modifier properly. you need to deselect all sub-objects (vert, edge, poly ect) then click on the modifier label "edit poly" then click on the skin modifier label.
Sub-object selection is passed up the stack, if you have one vert selected and then improperly exit the modifier only that one vert will be skinned.
It can also be messed up if your skeletal skin pose doesn't match the original position of the mesh. You should always set your "skin pose" (select bones, hold alt, right click, set skin pose/assume skin pose) so you can always pop whatever rig in and out of the original skin pose.