Relying only on the measured deflection voltage to measure the AFM tip-surface interaction is risky, as the loss of the signal may not be obvious. In order to validate incoming photodiode signals, you should also monitor the total light hitting the photodiode. This is especially true in fluid cell measurements, as bubbles of air or buffer solution can deflect the laser enough to miss the photodiode completely.
As far as I can tell, the total photodiode voltage is not carried on one of the DB-25 lines connecting the MultiMode to the NanoScope controller (see the MultiMode internals page). It is displayed on the MultiMode LCD, so I monitored the lines connecting the main board to the LCD board to isolate the total photodiode line (LCD connector 2). I build a small connector to tap out that line (despite appearances, none of the huge solder blobs actually short anything out :p).
TODO: image of connector.
We sent the tapped line out through Auxilliary D (DB25 line 4), so we could tap it again at out main break-out box. Comparing this signal to the photodiode ground (DB25 line 12), the signal is actually inverted (-7V signal when there's lots of light, 0V when there's none).