In what Cocoa developed applications are you performing the 'Command <control> D' - mouse cursor over a word, sequence on?
Go to the 'System Preferences', 'Keyboard & Mouse' Utility and click on the 'Keyboard Shortcuts' tab. Scroll down to 'Dictionary' (click on the disclosure triangle, if it is pointing to the right). Are the check box'es of 'Dictionary' and 'Look up in Dictionary' marked with a check mark?; and, is 'Command <control> (
caret symbol) D' assigned to 'Look up in Dictionary'?
A sample of the applications that support the above keyboard / mouse sequence:
'iChat', 'Mail', 'Safari' - with a web page's source code window present ('View, View Source' menu item) or within a textedit (text entry) field, 'OmniWeb' - with a web page's source code window present ('View, View in Source Editor' menu item) or within a textedit (text entry) field, 'Script Editor', and 'TextEdit'.
Give such a try, and post your results.