Is the command is based on smbus?? Something like i2c_smbus_read_byte_data() ? Smbus protocol has register write operation before read to specify the register location. As you said that may be causing the issue. Did you find any i2c specific functions in your header file? Please share the header file you are using.
One more clarification required : How you have set up the hardware ? How you are connecting it PSoC to your PC ?