OK, I wanted to post a reply just in case anyone else runs into this.
First thanks to Cal over at NT support, he was great. It turns out one of the other strategies (one in a closed source DLL) was causing this behavior. I did ask him to file some sort of bug on this condition though. Why should a strategy that is not being applied to the chart, be running its initialize routine (which is where that is set).
I can understand if MY strat was setting it, but it appears that NT runs all strategies initialize routines when the window pops up. I guess this is so it can read the variables/configs out of them but IMHO there should be another way around this, maybe not run initialize itself but just pull the properties? dunno.