When you enable Schedule or Schedule+Open shifts, Fareclock switches to a new Shift-based paradigm where all punches for a shift are grouped together into a Shift Card. Punches created before Schedule shifts are enabled will not be visible by default in certain reports (i.e., Time Cards, Totals, Tardy), because those reports show data by Shift Card. In order to view those old punches, those reports have an option to "Turn off Shift View" as shown in the screenshot below. Note that if you turn off shift view, all punches will use default shift settings and not any new shift rules you set up.
If you edit or add any old punches, they will then be processed by the new schedule shift rules.
For complete documentation on setting up Scheduled Shifts, see the following help article: