Currently you use GTK_WIDGET_UNSET_FLAGS (window->notebook, GTK_CAN_FOCUS); quite often in notebooks. This is cool, but notebooks (still) heavily rely on focus, for example for the arrow buttons with scrolling tabs. A better idea might be a "button-release-signal" on the notebook that moves the focus back to the vte widget, that will make the focus code inside a notebook work again while not bothering the user with a focus tab after a click.
Feel free to submit a patch. :-)
I knew you were going to say that... Will test it a bit in Mousepad before creating a patch for terminal.