Ted,

 Ag leader does compensate, as you think it does, for "less than all booms ON" when looking at minimum GPM. This was one of my first questions, to Ag Leader personnel, when I first bought my liquid control module and was programming in my settings. They assured me the software takes whatever boom width is "currently ON" and internally adjust its minimum GPM.{I have different boom width sections, like 11.6 ft; 7.6 ft and 3.3 ft, and Ag Leader Integra does fine, when watching a manual pressure gauge}

To original post:

I have idea, but I'm just guessing; I wonder what your "Rate Off" setting is for your Flow Control Valve? {Close or Hold}

Note: My 3pt sprayer is set on "Hold" = which means the Flow control valve (regulator) stays at the same setting, that it was at, right when the booms last shutoff.

Maybe your setting is set to "Close" ??? {when all booms are OFF}

Then there is this other setting about "Flow Control Delay", where it may not change setting (of flow control valve) for the first 1-2 seconds at the start of a pass.

Now, take the combination of settings for "Close" plus setting of 1-2 seconds on Flow control delay, and maybe your scenario, might happen.

I got this info, on a paper copy of "Ag Leader Quick Reference Guide 2006310 for sprayers" and I found it on the internet and will attach a .pdf copy to this reply. Maybe it will help you figure out your problem.

Ag Leader Quick Reference Guide 2006310_Sprayer.pdf (404KB - 194 downloads)