the communction server to server within same network will remain 1500 , but server over vpn will be fragmented to the MTU limit you place on router(VPN). This will cause slow down if servers are talking over VPN , best to change the MTU on the other machines in the network , this can be done via reg
HKEY_LOCAL_MACHINE\SYSTEM\CurentControlSet\Services\NdisWan\Parameters\Protocols\0
change the ProtocolMTU value.
http://support.microsoft.com/kb/826159 might also be of help