What game is this with? EQ1? There's a previous report of this issue in EQ1:
http://www.isboxer.com/forum/viewtopic.php?f=6&t=648My remaining question in that thread is whether the game itself is set to full screen, or windowed mode. You can determine this in the in-game video options panel (through Alt+O).
Alternatively if you hit the ` key in the game to pull up the in-game IS console (or the hotkey configured for "In-game Inner Space console hotkey" in your ISBoxer Character Set), enter this command:
This command will give a few lines of output, one of which is the current display mode and an indication of whether the game is in full screen mode, forced window (where game is in full screen but IS has forced it into windowed mode), or windowed. If it's in forced window mode, it might help to go through and set it to windowed mode in each game window (through the in-game video options panel!). You may need to close out the game and re-launch after changing this setting.
p.s. you're welcome to try out a previous build of Inner Space from the archives:
http://www.lavishsoft.com/account/is-archives.php -- but you will be trading off this bug for other bugs. For example, with older builds of Inner Space, forcing the game into a window was not a viable option and so the game would just crash if more than one window is set to full screen mode. And there's also cursor issues in some builds, where clicks may not occur where the cursor is (in some games in certain configurations)