Hi,
One of the biggest challenges in getting good chords is to choose the appropriate staves that contribute to the "correct" base chord. Sometimes only using two or three staves (rather than all 9 or whatever) gives the best result. It can take a little experimentation. It's also somewhat a "taste" thing, too, as some folks prefer more basic chords (it helps to choose something like "Rock" or to check only the chord types you want in the dialog box) while others want all the nuances and variations (in which case, check all the boxes
)
If there is a particular file that is just really giving you a hard time, please feel free to post it here and we can try to help you get what you're looking for.
ttfn,
Sherry