1. Everything is running smoothly when there are hardly any ships or econ updates to process.....so that's normal
2. After two hours there are probably hundreds of ships to take care of and hundreds of econ updates to prcocess so there will be a noticable slowdown.....also normal
What is your pagefile set to? I've personally tested SINS with many hardware/software and OS configs and have found that keeping one's pagefile size set to
at least 2.5 X the amount of installed RAM helps things.
Please realize that this game IS capable of bringing even the biggest, baddest rigs to their knees due to the size of games one can concievably have.
Also, SINS runs completely on one core. The only thing it uses another core for is texture caching, after that it's all on one core.
well.....there you have it!

the Monk