Aymen,
MTU should not be an issue. No need to modify the MTU for regular ethernet traffic, unless you're using IP storage such as iSCSI.
Let's narrow down the problem first.
1. Do you see packet loss/performance issues on other servers connected to the same N5K(s)?
2. Are you seeing any packet drops on the N5K interfaces or GATOs ASIC?
show interface e1/20 counters errors
show interface e1/20 flowcontrol
show interface e1/20 priority-flow-control
show system internal ethpm errors | egrep Ethernet1/20
show hardware internal gatos port ethernet 1/20| egrep -i err
I would check these counters on both the host facing and arrary facing interfaces.
3. What is the exact array that is FCoE attached?
4. Do you have a topology diagram?
5. What are the server side adapters, firmware and driver versions being used (include the OS on the host).
Regads,
Robert