There's a huge tension between audit-ability and ballot secrecy. You'd like every system to have a traceable log of events with timestamps so that you can go back and determine what happened if there is a problem, but when you have a poll book that says that John Doe checked in at 1:22pm on Tuesday and then there is a ballot cast at 1:27pm on Tuesday, it's a pretty easy deduction to determine who likely cast it. Note that this can occur with totally paper systems and voting limited to home precincts only, though those systems don't usually record millisecond-accurate timestamps like electronic ones do. It's a hard problem. Even things like party registration can be used to help identify ballots. For instance, if only one Republican votes in a heavily Democratic district in a given day or hour, you can pick it out of the mix. This is very easy for primaries where Republican and Democratic ballots are distinct.
There's a huge tension between audit-ability and ballot secrecy. You'd like every system to have a traceable log of events with timestamps so that you can go back and determine what happened if there is a problem, but when you have a poll book that says that John Doe checked in at 1:22pm on Tuesday and then there is a ballot cast at 1:27pm on Tuesday, it's a pretty easy deduction to determine who likely cast it. Note that this can occur with totally paper systems and voting limited to home precincts only, though those systems don't usually record millisecond-accurate timestamps like electronic ones do. It's a hard problem. Even things like party registration can be used to help identify ballots. For instance, if only one Republican votes in a heavily Democratic district in a given day or hour, you can pick it out of the mix. This is very easy for primaries where Republican and Democratic ballots are distinct.