Don't know if this is relevant to what you are experiencing, but .... I had my MK220 hooked up to two of my three batteries & wanted to switch one lead over to battery #3 & when I did I got a red light on that lead. Solid & constant, though, not flashing (on/off). When I cleaned the lead end off (some corrosion had set up on it) and then reconnected the lead .... the red light went off and the charging commenced.
If I remember correctly .... both green and red lights came on at the same time for that lead, when I first connected it to my #3 battery, but after cleaning the lead ring the red light did not come back on.