After today's commissioning meeting, JoeB pointed me to LLO alog 19578, where he describes the change that LLO made that seems to have solved the BS coil driver switching problem.

For whatever reason, it seems that the analog output is not zero until some time after the digital output has been zeroed. So, LLO added an extra 7 second wait time after the matrix has finished ramping.  I have now implemented this here, and we'll see what happens next time we try to lock.