The modules you have obviously have different versions of firmware, and I think that is where your problem is, but not for the reason you might first think.
Different versions of the firmware are generally backward compatible, as are the 2x64 and 2x41 version. That second digit in the firmware build is what’s causing your problem is my guess.
Firmware version 2241 indicates that the firmware is router firmware. Being a router the radio is essentially on all the time, so wen you try to communicate with it, it will respond.
Firmware version 2864 is end device firmware. Being an end device, the default state of the radio is to be in a sleep state. When in the sleep state, the radio will not respond to commands over the serial port, which is why you can’t communicate with it at times.
I don’t know anything about the Sparkfun boards, but when you try and Read the radio from the X-CTU, when the info box pops up, if you press the reset button, the end device will wake and the read will work momentarily. Once the read works, you can either change the SM parameter that is making the radio sleep, or reflahs with new firmware, something that doesn’t sleep by default.
If the board you are using doesn’t have a reset button, you can mimic the reset button by shorting PIN 5 to ground momentarily. Better yet, purchasing an interface board from Digi will ensure that all lines are connected as necessary, and all functionality is available on the radio.
Your new network will require that you have exactly one coordinator in it, and the other nodes will begin to associate from that point. If you don’t already have a coordinator, you can reflash on of your modules to be the coordinator through the X-CTU.