RDM6300 RFID reader does not work on stand alone breadboard arduino

We are making a circuit to run from the atmega328-PU microcontroller chip. I have successfully run the bootloader and can run sketches on the atmega328-PU on a breadboard alone (per Arduino - Setting up an Arduino on a breadboard , using the external clock). However, when I connect the RFID reader RDM6300 using wiring and the basic programming from Arduino Tutorials – Chapter 15 – RFID | tronixstuff.com , the RFID reader does not work. I tried changing the sketch to read pins 0,1 (instead of 2,3; on the atmega328-PU pinout this is pins 2,3 or 4,5) and still no results. The RDM6300 will function when connected to the same chip plugged into a Arduino board (the UNO board, with either a Duemilanove or genuino uno chip), but when it is plugged into a chip on the stand alone bread board it no longer functions (all other sketches tested work, and every other component of this sketch except the RDM6300 read function). We tried to power the stand alone chip with the arduino board 5V supply and still no difference.

Any help is appreciated. I hope that this is a dumb problem, but we have not found a solution after several hours.

Thank you.

Has the surface mount been bootloaded so its fuses are set the same as the other parts?

Thanks for the reply. I don't understand what that means. The atmega328 chip is just plugged directly into the breadboard and I have not set fuses, so I assume the answer to that is no.

How would I set up the fuses?

I have it set up on the bread exactly like in this diagram Arduino - Setting up an Arduino on a breadboard

I have also powered it directly from a 5V DC source bypassing the homemade power supply.

I have multiple RDM6300 and atmega328 (Uno and Duemilanove), all components work properly when on the arduino board, when moved to a breadboard only one part of the RDM6300 no longer functions as specified in the code.

Thanks again for the reply and I apologise that I don't understand it.

Are you saying that you have several readers and only one does not work but the others do?

You are not very clear in your explanation. How is your supply decoupling on your stand alone?