I don't really know much about I2C and TWI protocol, so I can't comment much on your issue. However, I'd like to share some probably related info.
1. I read in an article about RTCs, and they said the datasheet for this particular RTC chip does not state that they are using I2C to avoid paying royalties. They just say its a two wire protocol.
2. The DS1302 RTC chip uses a two wire protocol, but not I2C. I had to write some kind of bit banging code to get it to work. So there are some devices which do not implement standard communications protocol.