Hello Bharath,
What reference are you using? remember to measure VREF, VREFH and VREFL by using VSSA as reference.
Next image shows different positions for S1, S2 and S3 and what voltage is using every module, also notice that VREF pin should be 1.2V in your current configuration (S1 On, S2 Down, S3 Down):

So Vref is used as output (remember to enable VREFBUFOUTEN bit on SIM_MISC_CTL register).
I also corroborate this configuration by using vref_test example located at <KM128SWDRV_R4_1_2_PATH>\build\cw_10_6\projects\vref_test and it worked well.
How are you measuring this reference?
Regards,
Isaac