Finally I've found some people with the same problem. However I've found that installing KB885835 already causes this problem, Ryan might remember me posting this on his forum. I just copy the unpatched sp2 mrxsmb.sys (version 5.1.2600.2180 I haven't bothered to find a newer one) in my clean.cmd script. At first I thought it was because I used Nlite on my iso, but then I checked with a clean sp2 install with ryan's hotfix pack and found I had the same problem, missing folders, files and empty folders. Let's indeed hope there is a hotfix on the way, I don't really fancy checking each new update for another bugged mrxsmb.sys.