Laurent,
For what it's worth, I have a dual CPU server, running SME 5.5 with update 2 installed. It was a fresh install of 5.5, I loaded the first update as it was immediately availble after the initial install, then I loaded update 2 when it was released.
It's a generic box, a Tyan MB, dual PII - 233's, I'm using an old Proliant 2/P raid card and 3 huge 20GIG drives in RAID5 array, 384meg RAM. (incase you're interested in taking a look:
http://www.dgwebhosting.com/sysinfo).
PPro's aren't supposed to be plagued by needing the same stepping codes (PII & P3's MUST be same step code, +/- 1), but I have heard there are certain instances where this may be a problem, don't recall the specifics though, it's supposed to be up to the system's BIOS.
Have you tried flashing to the latest BIOS version on your MB? Just a guess.
Dave