Scroll wheels and scroll balls work as expected in CheckBook on our test Macs. Scroll wheel "events" are automatically passed to and handled by Apple's Cocoa classes, including the table and outline views we use in CheckBook, so we're at a loss to explain why your scroll wheel is not working there. It's eerily similar to the uppercase issue you reported previously. The basics are the same - events that are automatically handled by Apple's classes are not working on your Mac but they work properly on others.
Can you test a small example application from Apple to see if the scroll wheel works? I've placed a build of Apple's OutlineView test application at
http://www.splasm.com/special/checkbook ... ew.app.zip . If you launch this application and expand the top level element by clicking on the triangle at the top left of the list it will show you the files on your hard drive. Would you try scrolling through that list with your scroll wheel and let us know what happens?