The problem with the SDcard is known. There was a bad batch of SDcards from the supplier. About 300 were shipped and most have been replaced. It was difficult to track down the units sold through SmartGuys. In any event, replacing the card is straightforward and I don’t believe has anything to do with your problem.
Reflashing with firmware compiled using the Arduino IDE on the other hand has a lot of potential to cause problems. Your firmware does not seem to be able to communicate effectively with the RTC.
I can’t really support that firmware as it’s out of my control. Assuming the version that you flashed still has the ability to upgrade itself, I would recommend that you install the official distribution of 02_08_02 using this manual procedure.
Then delete both datalogs and the integrator and recreate the integrator.