Illustrator CS on my 10.4.1 install does the same thing when opening a new document. Takes a looong time. Illustrator 10 does not do this.
Also, be sure to check the ACIB box in clipboard preferences. If you don't and you try to copy and paste between applications you will get crashes and lock ups. This pleasant little change in Tiger left me floundering for a while.
Anyway, the short of it is that Illustrator CS SUCKS IMO.
I hope CS2 is better...