Ah.. right. I remember that this possibility dawned on me when I went upstairs to calculate finesses that day. I meant to tell you that I didn't check that the polarization was still S---sorry.
I re-measured the mirror transmissions for 45S for all the candidate mirrors for the cavity. The Y1 45P mirrors that were borrowed from the 40m have very low transmission for 45S. I think that when they were measured before, the polarization had been rotated at the wave plate just after the faraday, and this is what gave the higher transmission values for the 45P mirrors. I rotated it back to S using one of the good polarizers and power meter. I have labelled each mirror with a number and the measured transmission.
Mirror 1: BS1 - 99 - 45S, 2". Old input mirror from the gyro. Power in 115.4mW. Power transmitted 0.657mW. Transmission 0.57%
Mirror 2: Y1 - 45S, 2". Old output mirror from the gyro. Power in 115.3mW. Power transmitted 19uW. Transmission 165ppm.
Mirror 3: Y1 - 45P, 2". From the 40m. Power in 115.1mW. Power transmitted 13uW. Transmission 113ppm.
MIrror 4 Y1 - 45P, 2". From the 40m. Power in 115.3mW. Power transmitted 20.2uW. Transmission 175ppm.
Mirror 5: Y1 - 45S - 6.00m, 1". Old curved mirror from gyro. Power in 114.9mW. Power transmitted 15.3uW. Transmission 133ppm.
Mirror 6: Y1 - 45S - 6.00m, 1". Old curved mirror from gyro. Power in 115mW. Power transmitted 20.5uW. Transmission 178ppm.