Dual Core Problems?

In my quest to find why my game minimises and locks up after 30 mins i was looking at the processor performance. As its a dual core it has two graph windows, when the game is running in its minimised locked up mode the first core is running at max (total usage 50%) could it be its only using one core to run the game and can't handle it? Only recently got my new pc so i am still understanding how the dual core works.

The processor is a Core Duo E6400 2.1ghz.

Check out this post. Let us know how you do.
Also take a look inside your case it may need to be cleaned out.
Dust can overheat and shut down the sim.
Maybe you can add another fan or two.

http://flyawaysimulation.com/postt21628.html

Have you properly activated the software?