I swapped the pins in the JST and things are good now. I have asked Sales to cancel the replacement. Is swapped JST polarity a common issue with https://www.adafruit.com/product/727? Also, I find no polarity indicators on the CLUE board itself. That might be a good addition in the future. Thanks all!
Can't photo the item anymore as I swapped the leads (pretty easy to do if you have a VERY pointy stick -- titanium toothpicks work well). I'll try to remember if there is a next time :)
On a battery holder you can remove the batteries to avoid the risks of shorts but I used a wooden cocktail stick because that's not an option with a LiPo and something non conductive is safer.