It's the battery. Remove the top control circuit board from the cover. Flip it over. The battery is a CR-2025 button style battery.
How did I come to that conclusion? The reason I asked if your system comes on at 6 am is that if the unit reset to 12:00. When you checked it at 1 pm, it read 6:58.
Your pump starts at 6 am, so by 1 pm, that's 7 hrs.
From 12:00 to 6:58, that's almost 7 hrs.
PLEASE let me know if this did not do the trick.