Dennis,
In large installations, I've always found it helpful when diagnosing LAN issues to isolate floors and departments first - using routers or with devices that can do transparent bridging. That way, you can walk through each dept/floor testing for the issues, and hopefully find only one location its still affecting.
Its entirely likely that there's either a loop of some sort or a switch has gone off the deep end.
If you'd like, let him know if he wants to drop me a mail, I can walk through details about the situation and hopefully help him narrow it down.