I was testing the JChemPaint applet with some disubstituted cyclic compounds, like 1,2-cyclobutane, when I founded that the generated chiral SMILES for the (1R,2S)-1,2-dimethylcyclobutane and (1R,2R)-1,2-dimethylcyclobutane isomers were the same.
It seems that the applet have some problem in generating the correct chiral SMILES for (1R,2S) or cis isomers of cyclic compounds, that have an carbon atom described with the @@ notation.