I wonder if you ever got around to solving this issue. I'm trying to interface a DS1307/3231 over I2C and the module doesn't respond. Here's what I see on the logic analyser:
The clock frequency is 200kHz which should work with DS3231 but not with DS1307. For comparison, here's the same module interfaced to an Arduino:
The clock frequency in this case is 100kHz. Any ideas? How do I change the I2C clock frequency on the board?