My theory is as follows. Intense Debate works by replacing your WordPress standard Comment System through javascript. But if a visitor OR spam bot comes to your blog with Javascript disabled – they will be presented with a standard WordPress Comment System provided by your blog. Therefore the comments showing as SPAM on the main dashboard page were most likely left via the standard comment form not through intense debate. Becuase of this we still need to have antispam plugins enabled to deal with this & that is why they don’t show with ID activated. When I installed ID I deactivated GASP (Growmap Anti Spambot Plugin) as I thought I wouldn’t need it. After some experimenting to try & figure this out I have just re-activated GASP which gave me virtually no spam before ID installation so I will see if this proves my theory.
Hope this helps (unless I am wrong with my theory :-))