Here's the latest response from Line 6 tech support:
"The volume will reset itself every time you switch presets for this amp. It really has nothing to do with the Shortboard, more so the features of the amps firmware. This is not something we can change anytime soon, since our customers requested to have this feature available......It will be the same behavior no matter what pedal-board you choose to use."
This tells me the FBV 3 will have the same problem. I replied back that, as one of their customers, I don't see this as a feature I would want to use and that I would like to have the option to choose whether the amp or the volume pedal acts as the master volume when changing presets. As the "Ultimate Stage Amp," it doesn't allow the player to be in full control, the amp is. Very disappointing.