Native Vlan Effect on the Overall Network Performance

Dear Experts,
I would like to know that did Native Vlan affect the overall Network performance and make the whole network slow and can be cause for all Network devices to be failure or disconnect. I am facing this issue for the network that after apply Vlan dot1q tag native" in global Config the user disconnect from the network and also the devices.
Kindly assist on this issue with the practical scenario and result oriented conclusion.
Further I have following Devices in the Network Catalyst 4500, Nexus 5548, FIC 6248, UCS 5018 and Catalyst 3750.
The issue is this the VLAN 50 which is for UCS is not able to access from the LAN network even we added the VLAN 50 on all the Switches and it propogated to whole network so we  make Vlan 50 as Native and added "switchport trunk native vlan 50 on trunks ports from Nexux 5548 to Fabric Interconnect and to Core Switch 4500. After added vlan 50 as native vlan we can access the UCS from LAN.
But after adding native vlan 50 on all trunks the Network Administrator complaining that network is slow and few servers are disconnecting.
here for the information that server vlan is 1.
Waiting for the answer.
Thanks,
JH
Thanks,
JH

Hello.
1. Could you please draw interconnectivity diagram of all the devices?
2. Could you chose any LAN device (on the same switch as UCS) and post here running config of the device that interconnects them?

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