we have come across a couple cases where paid and unpaid break are not registering properly. 

A solution to this is to make sure that you have all your breaks documented in the automation reminders and paid breaks form.

Automation looks at the Breaks 1-3 as place holders, so if you have a manual lunch you will want to add that in your break series so the system can count the amount of breaks and code them as paid or unpaid on the time cards. 

Example:

The first and last breaks are on Auto as paid breaks so the system is going to take that time and automatically punch employees in/out for those two breaks, 

Notice that the lunch break is a duration of time  in between the two auto breaks but is set to manual. This is just so the system knows that a second break is going to take place in the day but it needs to be unpaid.  

Once all your breaks are filled out remember to apply to the employees and hit save. Now your breaks should all be documented in the correct order.