I have found a grouping of compounds where the stereochemistry of the molecule does not transfer properly when using name->structure (I ran them through chemicalize.org to ensure newest version was being used).
1-((1S,2S)-1-methoxy-1-phenylpropan-2-yl)pyrrolidine (returns (1R,2S) instead)
1-((1R,2R)-1-methoxy-1-phenylpropan-2-yl)pyrrolidine (enantiomer of first molecule, returns (1S,2R)
(S)-1-(2-methoxy-2-phenylethyl)-4-methylpiperazine (returns compound without stereochemistry)
1-((1S,2S)-1-methoxy-1-phenylpropan-2-yl)-4-methylpiperazine (similar nitrogen based functional group with same problem as first molecule)
1-((1S,2S)-1-methoxy-1-phenylpropan-2-yl)urea (very different nitrogen containing functional group with same problem as first molecule)
(1S,2S)-N,N-diethyl-1-methoxy-1-phenylpropan-2-amine (very similar molecule to the above, but DOES return the correct structure)
Let me know if you need more information to track down the issue.