Hi kaoha, and Welcome to SpywareHammer ;D
I have never seen this unusual (not to say annoying) effect in any version of Photoshop I've used, so I'm shooting in the dark here.
First, I suggest you install the latest CS4 update
if you haven't already. Also, check you have at least 512MB memory and the latest drivers for your graphics card.
Click the double arrow at the top of your Toolbox to revert to the default single column view. Now go to Window and uncheck Tools to hide the Toolbox. Next, go to Edit, Preferences, Performance and make sure 'Enable OpenGL Drawing' is unchecked. Finally, go to Windows, Workspace and select 'Essentials (default)' or, if that is already checked, select 'Basic'. (Silly as it may sound, there are things in Windows and, I suspect, Windows applications that don't 'take' until they have been toggled off and on).
Now close PS and re-open it. Go to Window, check Tools again and let me know if the Toolbox is behaving itself.