Upon Ushiba's suggestion we looked at the raw inputs the the REFL QPDs. Sure enough the whitening stage on QPD2 segment 3 and 4 in both I and Q channels are not engaged. See the attached plot.
Red green and blue on the top two plots show expected behaviour with the raw channel (IN1_DQ) being boosted at high frequency with whitenning. In the lower 2 plots red, green and blue (quadrant 4) are all overlapped showing no analogue whitening was engaged. The same is true for quadrant 3.
It is strange that segments 3 and 4 on both I and Q channels did not engage, we will check tomorow.