Try looking lower on your post for G55. I just did a test, selecting work coordinate 2 (G55). In the setup line (N10 below) it outputs G54, Then a few lines down (N24) you can see G55. I would expect it to output G55 in the setup line too, but it should run okay.
(T15 D=0.5 CR=0. - ZMIN=-1.5 - flat end mill)
N10 G90 G54 G64 G50 G17 G40 G80 G94 G91.1 G49
N12 G20 (Inch)
N14 G30
(Finish Pockets)
N18 G30
N20 T15 G43 H15 M6
N22 S16000 M3 M9
N24 G55
N26 G0 X15.0825 Y12.065