There's another reason to avoid the defaul VLAN:  with Cisco switches VLAN 1 only supports standard frames (1500 bytes).  Since it's the default VLAN, Cisco will attempt to deliver every packet, including jumbo frames.  When the switch is busy, larger packets may be dropped (leading to inconsistent behaviour with jumbo frames).  The MTU defined for other VLANs will be enforced (correct behavior will pass jumbo frames every time, OR none of the time). This frame inconsistency can be difficult to troubleshoot - I had two W2K3 servers connected to my SAN.  Both servers could discover, connect, and partition their volumes, but one would always disconnect when I went to format it (the other worked).  The working server connected via standard frames while the problematic one connected at 9000 bytes.  Setting the server's NIC to standard frames immediately resolved the issue (further testing with a different VLAN showed that both servers could work properly with jumbo frames). I was able to reproduce those results with a PowerConnect switch, and understand many vendors follow Cisco's lead regarding this behavior.
Why do you recommend to set aside a VLAN for jumbo frames for data between ISCSI hosts and the EQ?
Q about jumbo frames and setting up separate vlan 