Get the schematic drawing previously mentioned - it shows the wiring connections and will help clarify the following.

Because the same digit is missing on the paired displays it is very likely to me - almost certain - that it's a stobe issue. 

When you say third digit - do you mean hundreds?  If so it's strobe 4, this is on pin 9 of the connector on the rhs of the master display. Pin 1 is at the bottom, pin 18 is at the top and not used.  (all this is shown on the drawings which is why you need them) Examine the wiring associated at each end of this connector - follow the wire to get to the mpu board end.  You might be able to clean up the pin with a bit of scraping - but this is only temporary. Try it to see if any change.  It might also be a one of the stobe inverter IC's on the rhs of the master display IC1, 2 & 3  - are they socketed? If so you could try swapping one to another position - preserve the orientation. If another digit plays up it is the chip, a 4069 which you can get at Jaycar.