You should check that your custom view has constraints (or an intrinsic content size) that completely define the height of the view. If they don't, these views are collapsing down to 0 heights (this same thing has happened to me before).
You can check if this is happening by:
[stackView insertView:myCustomViewController.view atIndex:0 inGravity:NSStackViewGravityBottom];
[stackView layoutSubtreeIfNeeded];
NSLog(@"%f - %d", NSHeight(myCustomViewController.view.frame), [myCustomViewController.view hasAmbiguousLayout]);
With StackView, you'll see that the later ones print "0 - 1". The heights are 0, and they're ambiguous.
Vertical NSStackView's will only position views vertically, but won't give specific heights. (Same for horizontal stack views and widths).