After a long ride both my wife's and my Rad Runner's don't want to charge. The power light comes on so does the Green charged light. However we've discovered if we wait just a few minutes and then connect the charger they start charging.
If you're putting them on the charger right after you get home after being worked hard, the battery and/or controller may be too hot to properly accept a charge and are thermally-protecting themselves until they cool down. I've never seen this on my MiniST and if both your bikes do it, that would be my conclusion.
It's always good practice to charge batteries when at room temperature, neither too hot nor too cold.