its the text margins in the allprogsbackground that aligns the allprogs arrow (the one you are having troubles with) and its a case of trial and error sometimes, basically you will have to keep adjusting the setting until it sits where you want it. you have to have 3 images for the all progs arrow, the first is normal state, the second and third are mouse over. the pressed function dosent work. play with the left text margin that is the only one you will need to align it back to how you like, make sure the top, bottom and right margin is set to zero.
a startmenu will grown and shrink according to how many programs you have on your startmenu or pinned to the startmenu. changing the number in the startmenu properties/customize area.
also check the size of you userpane, making that smaller makes the skin smaller, same for the bottombar