Especially, as Roger points out, on a new game start.
(You may also notice that your Gravidar is blank for the duration, and then suddenly blinks to life after the pause ends and the universe populates with jobs and life).
The more things you have installed, the longer the pause tends to be. It tends to take 10 seconds or so on a new game for the pause to end on my machine, and then around 5-10 seconds after loading a save.
It usually goes:
A few seconds of basic activity -> Pause -> Continue as normal.
The only time you really have to worry about the pause is, if on starting a new game, you don't have any equipment, money, or reputation set.

(Edit: Or if it takes a very long time. Each machine has a different personality and equipment setup, though, so I can't speak for machines other than my own.)
I can also mirror his point on the necessity of "Thereshallbewings", as I played X3TC for a year before even realizing you were "supposed" to enable the Script Editor.
I tend to enable it these days anyhow, though.
