The AI button and the select all buttons in the bottom right corner of the BGII main window is missing most of the time.
This seem to be because the window along the bottom (GUWBTP18.MOS background) overlaps the window down the right hand side which has the buttons in it. I suppose it works properly in the original game because it does the window stacking in a different order. Making the bottom window a bit shorter fixes the problem.
This happens on Linux anyway.