It sounds like you did some customizing on your Window Layout region sizes. The issue you're having is that the aspect ratio of your main region is NOT the same as your other regions, and ISBoxer is rendering them at the main region size. If you want them rendered at the size you configure per region, uncheck the Swap option in your Window Layout. If you want the Swap option you'll either have to correct the aspect ratio (i.e. resize the main region, it can be bigger than the others but the ratio of width to height should be the same) to fix your display issue, or let them be smashed.