I looked over the mechanical drawings of the high power attenuator.  The position of the mount holding
the thin film polarisers is largely set by two dowel pins in the base and the machining tolerances.
However the nominal angle of incidence of the design is 55.014 deg.

    The thin film polariser coating has a measured transmission of 99.552% and 0.036189% for p and s
polarisations respectively, which is a ratio of ~2750:1.  There is no information about the coating's
sensitivity to incident angle but generally speaking these sort of coatings do tend to be a little
sensitive to incident angle.  That said, it might just be that the beam alignment into the high power
polariser is off a little.