I take a file, run Melodyne and I get one set of chords reported. I drag the same file (not the copy that Melodyne analyzed) as a WAV file into scaler 3 in Studio One 7.2 and I get a completely different set of chords. Why would I get two different chords sets?
It might help to share the results here. Chord names are a little quirky in some cases
There are many times that the chord names are ambiguous and open to interpretation. Even with plain MIDI, if I enter the chords from Scaler into the chord track in Logic, it can arrive at very different chord names than Scaler. The largest discrepancy is that Logic will simplify inversions to basic triads. Am/C will just get you Am in Logic for example. It also has problems with things like Am7 and Am9. No telling what you would get with Am9/C.
You really just need to sit down and check to see if the chords that both are coming up with actually contain the same notes. Chord naming often depends on context.
If you are using audio as the input you may be seeing differences in how the two programs analyse audio. Audio to MIDI is not a 100% accurate process and can be pretty terrible for some source material..