It seems that when starting up the SMB service on OS X Mountain Lion Server, there is a race condition and some of the prerequisites may not get started up in time for SMB to properly initialise. Fortunately, there’s a relatively easy fix over here: http://oceansidecoding.wordpress.com/2012/06/13/smb-and-lion/ Essentially, if you touch the SMB preferences plist, then launchd restarts SMB. If this is done after the servers’s started up properly, then SMB initialises and everyone can connect.
touch /Library/Preferences/SystemConfiguration/com.apple.smb.server.plist
The link above shows how to put this in a launchd plist so that 60 seconds after the system is stated up, the SMB service is restarted and everyone’s happy.