@Walt - I wonder if your issue is similar to what was reported previously in this thread above (by someone who had such a crap attitude that I didn't bother investigating). Rather the opposite of your useful analysis of course.
Multiple series columns. Ugh. I was in two minds about how or whether to even support them in this plugin, and clearly you have had enough problems to decide they are not worth the pain they cause. I haven't tried your scenario to see for myself (I don't use multiple series columns myself) so I'm not 100% clear on the issues as yet. As I possibly misunderstand it there seems to be two problems:
1. That when you flip to manipulate a different series column, changes are still being applied to the "initial" series column (unless you "remember" to lock the values before switching)?
2. Something funky may be going on in the sort order.
I'll be honest - if we can't figure out a way to make this "work" that is acceptable for people with multiple series columns, I would rather rip it out and go back to just supporting the main series. However if there is a way to make it work then I can quickly look at it.