Jeba, I looked at your MX box. 
I don't see router-id configuration but still commit go through fine. All contrail generated config is pushed successfully.
You said, this is happening in latest build. Please let me know the JUNOS Version.


root@cmbu-sydney# run show version     
Hostname: cmbu-sydney
Model: mx480
Junos: 14.2I20150528_0300_ssivaraj

root@cmbu-sydney# show | display set | match router 
set groups re0 system backup-router 10.87.159.254
set groups re0 system backup-router destination 0.0.0.0/0
set groups re1 system backup-router 10.87.159.254
set groups re1 system backup-router destination 0.0.0.0/0
set routing-options router-id 172.16.95.1
deactivate routing-options router-id
set routing-instances csol1-vrf routing-options router-id 172.16.95.1

root@cmbu-sydney# run show system commit    
0   2015-06-13 17:33:00 PDT by root via netconf

root@cmbu-sydney% date
Sat Jun 13 17:36:03 PDT 2015

root@cmbu-sydney# show groups __contrail__ | display set 
set groups __contrail__ interfaces irb gratuitous-arp-reply
set groups __contrail__ interfaces irb unit 12 family inet address 172.16.90.1/24
set groups __contrail__ interfaces irb unit 5 family inet address 172.16.100.1/24
set groups __contrail__ interfaces lo0 unit 0 family inet address 172.16.95.1/32 primary
set groups __contrail__ interfaces lo0 unit 0 family inet address 172.16.95.1/32 preferred
set groups __contrail__ forwarding-options family inet filter input redirect_to___contrail__ad484e9f-fb9f-4fce-a2a1-fc5c6f473e_vrf
set groups __contrail__ routing-options route-distinguisher-id 172.16.95.1
set groups __contrail__ routing-options autonomous-system 64513
set groups __contrail__ routing-options dynamic-tunnels __contrail__ source-address 172.16.95.1
set groups __contrail__ routing-options dynamic-tunnels __contrail__ gre
set groups __contrail__ routing-options dynamic-tunnels __contrail__ destination-networks 172.16.80.0/24
set groups __contrail__ routing-options dynamic-tunnels __contrail__ destination-networks 172.16.80.3/32
set groups __contrail__ routing-options dynamic-tunnels __contrail__ destination-networks 172.16.80.2/32
set groups __contrail__ routing-options dynamic-tunnels __contrail__ destination-networks 172.16.95.1/32
set groups __contrail__ routing-options dynamic-tunnels __contrail__ destination-networks 172.16.80.4/32
set groups __contrail__ routing-options dynamic-tunnels __contrail__ destination-networks 172.16.82.200/32
set groups __contrail__ protocols mpls interface all
set groups __contrail__ protocols bgp group __contrail__ type internal
set groups __contrail__ protocols bgp group __contrail__ multihop
set groups __contrail__ protocols bgp group __contrail__ local-address 172.16.95.1
set groups __contrail__ protocols bgp group __contrail__ hold-time 90
set groups __contrail__ protocols bgp group __contrail__ keep all
set groups __contrail__ protocols bgp group __contrail__ family inet-vpn unicast
set groups __contrail__ protocols bgp group __contrail__ family inet6-vpn unicast
set groups __contrail__ protocols bgp group __contrail__ family evpn signaling
set groups __contrail__ protocols bgp group __contrail__ family route-target
set groups __contrail__ protocols bgp group __contrail__ neighbor 172.16.80.2 family inet-vpn unicast
set groups __contrail__ protocols bgp group __contrail__ neighbor 172.16.80.2 family inet6-vpn unicast

----

06/13/2015 05:31:45 PM [csol1-node2:DeviceManager:Config:0]:
send netconf message: <config xmlns:xc="urn:ietf:params:xml:ns:netconf:base:1.0">
  <configuration>
    <groups operation="replace">
      <name>__contrail__</name>
      <protocols>
        <bgp>
          <group operation="replace">
            <name>__contrail__</name>
            <type>internal</type>
            <multihop/>
            <local-address>172.16.95.1</local-address>
            <family>
              <route-target/>
              <inet-vpn>
                <unicast/>
              </inet-vpn>
              <evpn>
                <signaling/>
              </evpn>
              <inet6-vpn>
                <unicast/>
              </inet6-vpn>
            </family>
----
----

Please re-