I've got an R-enantiomer, and CDK recognizes that. But when depicting, it's inverted to S:

Tried CDK 2.8, 2.11

I use a MOL, it's clockwise Cl → O → N, though notice that the bonds don't have CFG. Not ideal, but that's what I get when converting from InChI=1/CH4ClNO/c2-1(3)4/h1,4H,3H2/t1-/m1/s1 (if I depict directly from InChI, then it's fine).

  CDK     0411251702

  0  0  0     0  0            999 V3000
M  V30 BEGIN CTAB
M  V30 COUNTS 5 4 0 0 1
M  V30 BEGIN ATOM
M  V30 1 C 0 0 0 0 CFG=1
M  V30 2 Cl 0 0 0 0
M  V30 3 N 0 0 0 0
M  V30 4 O 0 0 0 0
M  V30 5 H 0 0 0 0
M  V30 END ATOM
M  V30 BEGIN BOND
M  V30 1 1 1 5
M  V30 2 1 1 2
M  V30 3 1 1 3
M  V30 4 1 1 4
M  V30 END BOND
M  V30 END CTAB
M  END

As a result I think either the bond CFG must be set (ideally), or the depiction needs to be fixed.