Latency observed when traffic goes via NetScaler cluster. When going through the Network trace it was observed that some of the packets was not reaching the flow processor node. 
Environment:
1. Two node cluster
2. NetScaler VPX 10.5.53.x
3. running on Hyper-V

After enabling the Jumbo Frames and MAC spoofing on HyperV has resolved the issue.
Links for enabling Jumbo Frames on Hyper-V
http://www.altaro.com/hyper-v/how-to-enable-jumbo-frames-for-hyper-v-guests/

Known issue related to steered packets getting dropped:-
http://support.citrix.com/proddocs/topic/netscaler-release-notes-10/ns-rn-known-issues-78-x-con.html
Issue ID 0324865 (nCore VPX): In a cluster of VPX appliances that are deployed on HyperV, steered packets are dropped. Workaround: Enable MAC spoofing on the HyperV backplane interfaces.
 

---

Problem Cause

Customer has two node cluster. 
For certain TCP sessions the Node1 was acting as FP(flow processor) and it's working fine. However, for some TCP sessions Node 2 is acting as FP (flow processor).  So when the packet reaches Node 1 which is acting as a FR (flow receiver) for certain TCP sessions should forward that packet to Flow receiver via back plane . This is also called DFD steered packets. So in this case the packets were not getting steered to the FR via back plane . 
Since Jumbo frames and mac-spoofing was not enabled on the hyper-V, steered packets were not reaching the FR(flow receiver) node via backplane. 

This could be seen from "show cluster node" output, however this is not the symptom, but it's recommended to enable Jumbo frames for backplane.

exec: show cluster node
1) Node ID: 1
        IP:                  172.x.x.1
        Backplane:           1/1/2
        Health:              UP
        Admin State:         ACTIVE
        Operational State:   ACTIVE(Configuration Coordinator)
        Sync State:          ENABLED
        Priority:            31
        WARNING: Jumbo frames are not supported on this node. To support jumbo frames, set the MTU for interfaces of the backplane switch to greater than or equal to 1532 bytes
2) Node ID: 2
        IP:                  172.x.x.2
       Backplane:           2/1/2
        Health:              UP
        Admin State:         ACTIVE
        Operational State:   ACTIVE
        Sync State:          ENABLE