I don't own Aperture so I am not sure. But i know in iPhoto, iPhoto has it's own garbage that has to be emptied separately from the main Trash. Is it the same way in Aperture?
Would you happen to be running Mac OS X Lion? I found that Aperture started sucking when I installed Lion on my Core 2 Duo because it really pushed the CPU to the limit, but it ran relatively fast with Snow Leopard.