It seems that IllCS just doesn't like to read the default Startup files, either RGB or CMYK. I like to have the doc grid and rulers there by default - but no such luck.
CS is by far the biggest step backwards as far as breaking old functionality goes in Illustrator's history, I would say. So much stuff needs to be fixed, it's just crazy... sadly though, I can't see Adobe doing anything near like what Macromedia did to Dreamweaver MX - that kind of thing really increases love for a product.
I don't think I've ever found as much joy in a software patch as I have in the DW MX 2004 one - it totally made me want to go and re-explore things in Dreamweaver and just play with stuff to see how much faster and... well... COOLER it was now.
We might get a patch for Illustrator CS. Or we might end up having to buy Illustrator 12 (I hope they don't call it something stupid like Illustrator CS 2004 Professional XP edition X) to fix this version's deficiencies :-/