Protecting I2C bus with diodes
Looking at the datasheet datasheet, it seems like those diodes can have a significant reverse current -- up to several milliamps at 5V if they're warm. They also have a nontrival junction capacitance, on the order of 100 pF.

The main question is whether this is an AC problem or a DC problem. If the DC level is correctly pulled up to 5V but the rise times are too slow during transmission, try using stiffer pull-ups, no more than 1000 ohms. (You do have pull-up resistors, right? You need pull-ups for I2C.) If the DC level is stuck at 3.6V, try measuring the diode current with a multimeter to make sure they're not broken. You could also try removing the 100 ohm resistor.