I noticed that the fiber polarization (in wrong pol) at EY had drifted back up to 32%. The normal procedure for this is to turn the controller back on and adjust the settings; this never seemed to disturb anything. When I turned the controller on it made a funny noise (it sounded like the waveplates were moving rapidly), and BOTH EX and EY polarizations got drastically worse. I manually adjusted both polarizations, and they are back down now. I turned the box off. I did not want to turn the box back on. Clearly this is not good...
The temperature in the MSR were the polarizer is located is varying a lot more now with the change in weather (and between day/night). As I recall, it's pretty sensitive to temperature changes... and the MSR isn't really temperature controlled to a high degree of accuracy beyond 'not hot'.