I had so many problems using SMB. I found it imposiible to work with, kept getting the now infamous error -36. AFP comes with it's own problems, but as for the disconnecting error, I belive a registry hack on the server fixes it.
I haven't done this but I've been told that you can amend the reg...
HKEY_LOCAL_MACHINE\SYSTEM\CurrentControlSet\Services\lanmanserver\parameters\autodisconnect
Set this to ffffffff and the server will never disconnect clients.