if you are currently using the chord fingering type "Multi Finger" , try setting it to "AI Fingered" or "Fingered".
Interesting post, Chris. Why do you think this will help? With AI (which is my prefered fingering scheme) I sometimes get glitches when playing a chord with three fingers, because two of them (played early) produce a different chord. Example: press C-E-G for a C major and be late on the E, then you get a C1+5 glitch.
As I don't get these type of glitches when normally playing with styles, it seems that in style playing mode there is some timing tolerance before a chord is recognized. This makes sense, because humans are not capable of pressing ALWAYS several keys EXACTLY at the same time (tick). My reasoning is, that this tolerance is not applied when using Chord Looper. Of course, it's just a theory based on my observations.