That is the host syncing with the ai thread -- the more ships that are present in the galaxy, the longer it takes. Most of the time it will last 10 seconds or less, if that, but sometimes a bit more depending on hardware, etc.
On a dual core machine, having the game use 90% or even more processor is not entirely unexpected, though. The main simulation thread has the potential to use all or nearly all of one core, depending on what is going on, and the ai thread can use all or nearly all of the second CPU. With more cores you would never see much more usage than those first two, but those first two can be used quite heavily depending on the campaign.
But, with that sort if usage, that does not have to correspond to lag -- most pc games use near 100% of one core for normal operation. If lots of lag is happening at the start, you can pause to let it catch up. I am surprised that it would be lagging at the start on a 2.8ghz dual core at that low a number of ships, but it might be slower ram or a particularly busy simulation (big battle at the time of the ai sync) or something like that.
Version 2.001m introduces some performance improvements in general, so that might help if the lag is caused by a too-busy sim at the same time as the ai sync.
