All the algs in PitchFactor handle guitar chords pretty well except Synthonizer which is a mono-synth and Octaver which is based on old school analog octavers which are by definition monophonic. The one caveat is that complex chords can sometimes confuse the pitch tracking in Diatonic and Quadravox. It works pretty well for most common chords, but if your trying to screw it up, you can. The best solution for this is to use HarModulator or PitchFlex which can be explicitly set to a given interval (eg. m3rd, M3rd, …).
We did a fair amount of work improving the pitch tracking for this product and are currently porting that to the H8000 and Eclipse. It would be fair to say this product has the best pitch tracking of anything we've ever released.