If you set up auto lunch but have punches from the past you can 'regenerate totals' and the Auto Lunch punches will generate and be in the Transaction table.
Another report which will help to identify any abnormalities or to verify that the lunches are being correctly handled is the Time Detail Report:

Here we see the time of the punches, the Auto Lunch punch will always be made at the start of the days shift after the rules are met. As we see on the 15th I only was on the clock for 3.83 hours thus no Auto Lunch was deducted but the following day I had 4.5 hours on the clock so my half an hour lunch break was deducted.
Presume Lunch:
We now have set Auto Lunch up for our employees but some of them punch out for lunch at times so in order for us not to deduct twice for lunch we now set up our "Presume Lunch" rule. To make adjustment go to the Software Options window. Use the navigation window to open up the Software Options window by click on SetUp/Program Options.

Now we click on the Punch Rules tab to get to the correct screen where we make our Assume Lunch settings. In the picture to the right you see the "Presume Lunch if Off Clock" settings. They will be greyed out until you place a check mark in the box. All entries here are in minutes.

Our first adjustment will be the "Presume After"; this is the amount of time I have to be at work for the rule to come into affect. Here we have 180 minutes which translates to being at work for 3 hours or more be for the Presume rule will look at the punches.
Now the second line "Min" and "Max" is the amount of time in between the punches. We have a Minimum time of 5 minutes which means that if I punch out then back in within 5 minutes the Presume Lunch will ignore these punches and my auto lunch will be deducted if I fall into the Auto Deduct rules.
The second time amount we enter is the Maximum time of the off clock period to count as a lunch punch. Her we have it set for 2 hours; 120 minutes.
These settings mean that if I make a punch 3 hours after my in punch and another punch back in an hour later I will not get an Auto lunch deduction because the system will Presume that my hour long punch was lunch. The time span between my out for lunch and back falls in our rules of longer than 5 minutes but less than 2 hours.
Expand Short Lunch
These settings allow the program to calculate the worked time accurately but perhaps I am haphazard even more about my punches, you had set me up on Auto Lunch because I don't always punch for lunch but some times I do, so we covered that to insure that I don't get double "dinged" for my lunch break with Presume Lunch rules.
Still though things aren't right because I don't take a full half an hour punch for lunch so we can now set the application to "Expand" my short lunch to match what I my Auto Lunch deduct amount is in my Employee record.
We do this by checking the box next to "Expand Short Lunches" above the Presume Lunch settings. Use the Drop down to choose the correct amount to expand short lunch to.
These setting should now let you automate your lunch process and help insure accurate lunch break logging.