We never resolved it, got a new 4000 board and it ended up having issues as well. Now about to try on yet another board. I think its safe to say these new 4000Di boards are not as good as other versions.
I have the 4000T version in my machine and have ZERO issues with it.
I have several Mediators. The biggest issue I've had is that sometimes NO PCI cards are recognized at all. Re-seating the Mediator card itself usually fixes it for awhile.
I haven't had freezing or crashing otherwise, but I am using a 060 cpu. Perhaps it's different with the 3640 CPU card...