unicast flooding and arp table

[danlondon]

Hi,
I have 2 switches, a 5412zl and a 2848. They are linked via fibre GBIC's.
On the 5412 I have server1 and main raid. On the 2848 I have server2 and backup raid.
Every night the software on server 2 "pulls" the required files from the main raid via server 1.
However when server1 sends the files all the ports on the 5412 get flooded with unicast packets.
When I do a "show arp" on both switches they both list server 1 ip address but not server 2.
If i ping server 2 from a telnet session on the 5412 it responds and if I then do a "show arp" it is listed BUT the port is not listed.
I'm guessing this is why it is flooding.
There has been no recent topology changes.
What can I do to stop the flooding? (or in other words how do I get the 5412 to see what port it should send out on, I presume this would fix the problem?)
Thanks,
D.