1. A input clock or crystal should be valid before you write a new configuration (register map) to the RAM of Si5338
2. Writing new values to the IC should follow read-modify-write process via write-allowed mask. Here is AN428 and source code about programming.
3. I2C timing:
Hold Time START Condition tHD:STA should bigger than 4us for standard mode and 0.6us for fast mode.
Data Hold Time tHD:DAT should bigger than 100ns for standard mode fast mode.
4. If you simulate I2C via FPGA, please configure SDA to inout. Set SDA as output when write data, and Set SDA as input when ACK send to FPGA.