WTFoxtrot,
Can you show me some code from your VDX config, per se the interfaces switch ports connected to the VMware host servers? Maybe the port-channel configs from both VDX and Cisco, too.
How are you configuring the native Vlan on the VDX side (there are some options there you have to decide on.)
We used pvst+ mode on the interfaces of our Brocade MLX switch (lag) to VDX 6730s (vlag). For Cisco we were told to use pvst+ mode, too.
On the VDX, we are trying to deal with that 2500 byte MTU, now. Our firewalls and MLX are all set to 1500 (1548) MTU, and Microsoft says that our RDP disconnects on our HyperV VDI sessions are due to packet loss, TCP re-transmissions. I think the 2500 MTU is the culprit.