I'm not sure if this is a VirtualBox bug, although it doesn't occur with any other program. Basically, when I click on the 'pause' button, the simulation stops but CPU usage is still maxed out. The "new simulation" dialog, though, when not in Internet Mode, stops using CPU and pauses the simulation, so I use that as a workaround.
This happens with *all* sims and has happened since I started using Darwinbots.
(VirtualBox is a PC emulator much like VMWare or VirtualPC, I use it to run Windows for Darwinbots.)
Oh, and sorry if this is a known problem, I couldn't find it using the search feature.