Hi perfectprint, you aren't alone on this.
i gave up using Sonar's Chord Analyzer. instead i am using this alternative from Pizmidi.
http://www.thepiz.org/plugins/?p=midiChordAnalyzer its not a pretty workaround but at least it does the job.
1. insert this as an instrument in the instrument rack.
(uncheck all the ticks on the left of the panel, check the ticks of "Synth Property Page" & "Synth Rack View)
2. you should now see the analyzer in an open window.
3. insert a blank audio track.
4. set the INPUT of this AUDIO TRACK to " midiChordAnalyzer Primary Output Stereo"
5. from your MIDI TRACK, which is currently set to the "OUTPUT" of your synth, change it to the output of the "midiChordAnalyzer"
6. PLAY, and you should see the chords on the analyzer window. (you will not be able to hear any sound though)
hope this helps....