1) Are you using a Cypress FX2LP DVK or do you have a custom board, if so, please share your schematics.
2) Please probe the I2C lines and see if you are getting signals over them. Please ensure that you have used .iic file to program the device (not the .hex)
3) Do you see this behavior on only one FX2LP board, or do you see this on multiple devices?
I have a custom board in production already. Only one of the cards is having this problem. I have checked all pins for proper soldering, replaced already the eeprom. When loading the large eeprom I get a "succesful" message, but it won't read from it. I'm looking into it so I replace the FX2LP chip on the board. These boards a have very expensive componets and I don't want to throw it away because a faulty chip. I just want to make sure there is nothing else to check.
Please load Vend_Ax.hex firmware(present in FX2LP DVK examples) to RAM(using controlcenter) and pass the vendor command(0xa9 Dir-IN wValue-0x0000) and see if you are able to read the contents of the EEPROM. If you are not able to, then the EZ-USB is not able to access the EEPROM. Please check if the pull-ups on SCL and SDA are proper. While passing the Vendor commands probe the I2C lines to check if the Vendor command is passing through.