Oh crap, that was it. I should have rtfm again. The cowboy repeater mods the long tube, fast loader and maple stock, so I was just expecting the same. It makes perfect sense with the scope, you would not want that "applied" all the time. Nice mod, the .44 magnum really packs a punch... for a conventional weapon.
OTOH
I just picked up the Gauss Rifle and that is some serious firepower. I tried it out on a bighorn and OMG... that is a big beast and it knocked it down like it was a Night Stalker getting hit by a .357 magnum.
Did you apply the mod to the weapon? Pull up your Pip Boy and select the Trail Carbine - you should get, in the upper right hand area of the Pip Boy Screen, an indicator telling you which button to push to Repair or Mod the weapon (on the PC, the defaults are "R" and "X", respectively). Select "Mod", and the scope should appear on the list. Check it, exit the Pip Boy and you should be good to go.