I had a somewhat similair problem whit samba 3 a while back(on a small home-server, that is
Samba was running very slow, browsing the shared folders was really slow, and it was using quite a lot of resources.
In the syslog there where a lot of messages whit RT_SIGNAL_LEASE failures from samba.
After some browsing around I found out that putting
kernel oplocks = no
in your smb.conf fixes these messages, and samba is running at normal speed now.
this MIGHT be these case here, too.