If it's network related, it should be straightforward to diagnose it....
my process would start with port mirroring at the switch level the port of both machines to somemachine that can open a promiscuous interface, capture the packets, time correlate the captive packets again your logs... in samba I would just increase my log level (to scary levels) and pretty quick you will figure out if it's a host name resolution problem, some sort of tragic packet loss problem, or a security level issue.
My guess is that you have host resolution issues, becuase if things are just slow for the first time you browse for file (project manager) I would try to make it faster by makign the resolution quicker.
I'm sorry I can't be of much help if you are on a 2003 windows server or something, I sorta jumped off the windwos server bandwagon in the 90s.
Numa