Ron, BiaB's chord naming rules that I outlined above only effect whether a certain chord is named as a flat or with the equivilent sharp. You can see this in Audio Chord wizard by changing the "key sig" dropdown box - one chord can be G# if you have the key of E selected, and the same chord will be Ab if you have the key of Eb selected - but those are just two names for the same chord. It does not explain why Audio Chord Wizard gives you the "wrong" chords.

Here's a list of things that affect the chords that ACW reports.
1. the bass does not always play the root. I just recorded myself on All of Me, so I was able to compare the actual notes in BiaB to the chords that ACW found in the audio recording. In the 3rd and 4th measures there is an E7 chord, but on the 4th measure the bass was not playing an E, he was playing C#-B-G-E. On the first beat of that measure ACW saw C#-E-G#, which is a C#min, then applying the chord naming rules for the key of C, it called the chord Dbmin (which is equivilent to C#min). On the third beat, ACW saw G-B-D and E and called it a G chord. That's not what the chords are "supposed to be", but it matches the actual bass notes plus a couple of other notes that were being played at the same time. It was easy to see why ACW chose the chords it did, but the chords did sound funny when I played them back in BiaB.
2. Background sounds and percussion instruments can make pitches that are recorded as notes in ACW.
3. Musicians don't play only chord tones, and melodies don't just include chord tones. Sometimes it is hard to figure out what notes are the chord tones and which are not.
4. ACW can only resove 2 chords per measure. If the piece has more then results will be unpredictable.
5. If your bars are not aligned properly in ACW then ACW can be looking notes from 2 different chords.
6. Often a group of notes can belong to a number of different chords. Is C-E-G-A a C6 or an Am7? Maybe it's really supposed to be an FMaj7 but no one is playing the bass note one this particular beat. Maybe one of the notes is a passing tone or a tone from a percussion instrument and the chord is supposed to be something else altogether.

Jim