This is not the panel for the 727-100 is it? This is the panel for one of the Expansion Models isn't it? It is the only reason I can think of that would make it disappear.

Try this instead and see if this works.:

[Window03]
Background_color=0,0,0
size_mm=447,106
position=2
visible=0
ident=10005
gauge00=..\..\CS_B727-100\panel\Captain_Sim.p721.P12!P12_001_ap, 20,0, 427,106
gauge01=Cessna!Nav_GPS_Annunciator, 0,0,20,20
gauge02=Cessna!Nav GPS Switch, 0,20,20,20

The bold text is what needs to be added so that the 727-200/100F/200F have to access the AP in the 727-100\panel folder.

I think this will fix the missing AP problem.

Mark