Jorge,
I use the DS1307 and this problem already occurred with me in the past. My project is the POV Clock by Pimentel from community competition (look in this site). In my case was the current colapse, then I needed to increase my power (12 to 13.5v) because I was using a fet wired in the coil (transformer with air nucleus and it needed more volts to work fine. I don't know if when your circuit loose the data is because your hardware is consuming more current...but with me it occurred!
Other thing that may be the BROWNOUT RESET config. Is ON or OFF? Try OFF !
Pimentel
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