For some reason after the weekend, I found that the laser power on the south path decreased by about 300 uW. On checking power with a laser power meter, I found that a PBS, right after South EAOM and a half waveplate, is dumping more than half of the power as it is vertically polarized. The half waveplate is supposed to rotate the vertical polarization from EOAM into horizontal for cleaning by the PBS. I have rotated this waveplate to get maximum output from PBS.

Still, the loss at this stage seems much more in comparison to North Path.
Loss at North Path after EAOM  due to horizontal polarization at output = (354 uW)/(2431 uW) x 100 = 14.56%
Loss at South Path after EAOM due to horizontal polarization at output = (545 uW)/(1957 Uw) x 100 = 27.85%
I have checked that input polarization is correctly vertical for both EAOMs.(Only about ~1% light horizontally polarized for both paths at this point). Also, both EAOMs (New Focus 4104) are currently terminated with 50 Ohm terminators at their modulation ports.