Check your VSync setting in the game? If you're at 60Hz and VSync is enabled, FPS will be capped at 60. If it spikes to 100 on occasion, then it is not being FPS-limited by ISBoxer to 60, or VSync capped to 60. You might just not be able to pump out 120 FPS on all of your windows?

Also, ISBoxer's FPS settings override Inner Space's FPS settings. Whatever you set it to in the Inner Space configuration window is irrelevant when using ISBoxer.