I assume that it doesn't like my graphics card - i get a compiz fusion
icon in the menu but that's it.

Synaptic, apt, aptitude and add/remove all have different databases of
apps installed. So one is best to stick to one i gather. Aptitude will
remember dependencies and thus will remove them when you remove a
particular app. apt's autoremove and purge will also remove
dependencies but not quite so reliably as aptitude from what i can
work out. aptitude will however sometimes remove wanted items if one
has switched between apt and aptitude i've found. I just stick with
apt and use deborphan to get rid of dependencies - not a big deal if
one is upgrading every 6 month or year [i just do it yearly]. Synaptic
is great for installing but definately doesn't remove dependencies
from what i've experimented.