I removed the half-wave plate (HWP) that changed the polarization and was located between the shutter and the periscope at the very end of the PLS table (before Fig.1, after Fig.2).
Now the polarization is back to S.
I left the HWP on the PSL table just the side of the shutter. I saw a beam to RFAM and was careful not to block it by the HWP.
By the way, I noticed that the aperture of the HWP was only .5 inch. The beam diameter looked more than 1cm on the sensor card. Was there no clipping?