Fraser, not related to batch but I have noticed (and logged with OSI tech support) that the move from ProcessBook v2.x to v3.x introduced some anomalies in to the ProcessBook object model.
For example, rather than using the built in ProcessBook buttons for navigation I have used the SelectionChange event and based on some logic some displays are opened. In v2.x the newly opened display would get the focus but in v3.x the focus switches back to the original display - very annoying! Turns out I had to move logic to the click event, which meant the focus was retained on the newly opened display.
I then found out that when I opened a display from within another display, the display Activate event was not always triggering correctly (where I had some logic for display manipulation)...if I opened the display directly in ProcessBook the Activate event is fires fine. Never got this resolved, just put in some workarounds.
I would suggest you log it with Tech Support...if only we got to look at the ProcessBook source code
Fraser: did you get any luck sorting this one out?