There's a page on the ISBoxer wiki regarding performance: HOWTO: Tweak your framerate, just so that we that support ISBoxer don't have to continually repeat ourselves

The HOWTO starts out... "First of all, let us be clear: your framerate (FPS) with Inner Space and ISBoxer should not usually be significantly lower than your framerate without Inner Space and ISBoxer with the same size, number, and position of game windows. This guide should help you achieve at least the same FPS, if not higher."

Start there!