do you have remote console access i.e. DRAC or ILO ?
did you mention if any recent OS or other software updates like 5.3 to 5.4 or otherwise?
someone could be DOS'ing the server ???
do you run a firewall and drop bad traffic to the floor or is it wide open?
you havent mentioned what the various logs on the server tell you.
what about thermal issues?
recent BIOS update?
things in BIOS that should be turned off or changed ?
also, you might consider using some boot time kernel parameters to disable things hardware wise etc that are not absolutely necessary.
do you hard set NIC duplex in software?
i.e. ETHTOOL_OPTS="speed 100 duplex full autoneg off"
does it match the switchport? i.e. hard set? auto negot? cisco should be hard set.
is the switchport bad?
bad cable or cable ends?
bad fiber or fiber connectors?
mac address or arp issues?
the list goes on.
- rh