One of the most annoying things I’ve had to deal with is installing BES Express on SBS 2008. Way back earlier in 2010, I was mostly dealing with the 5.0.1x release. There were soo many bugs, so many issues, registry hacks, SQL queries that had to be run, it was just ugly!
One word of advice, always download the latest version of the software. Do not take ANY shortcuts on installing it. Either use the video tutorial that RIM has on their BlackBerry site, or use the guide from http://www.smallbizserver.net/Articles/tabid/266/Id/343/How-to-install-BlackBerry-Enterprise-Server-Express-on-a-SBS-2008.aspx
I don’t know how much is fixed, however after installing a 5.0.2 this weekend it worked flawlessly after the first install (keep in mind I always use “Blackberry Administration Service Authentication” instead of Windows Authentication because of an old known issue).
The link to the SBS document is broken. I don’t suppose you have a cache of the document do you?