I also had this problem. I found this worked for me. I am using an XB24 in a Adafruit XBee adapter shield, with FTDI Chip TTL-232R cable.
Connect your USB to TTL cable, or other connection method. Determine the COM port used.
Open X-CTU, select the proper COM port in the 'PC Settings' tab.
Then click on the 'Modem Configuration' tab.
1) Put a check in the 'Always update firmware' button.
2) Select your 'modem' type (for me- XB24)
3) The 'Function Set' and 'Version' were set properly automatically for me (XBEE 802.15.4 and 10E6). Change them if you need to.
4) Now REMOVE (yes, remove) the XBEE chip from the adapter. Now back on X-CTU , click on the 'Write' button. After a short wait, a window will come up saying it was unable to communicate.
5) Now insert the XBEE chip into the adapter. The window should disappear, and the firmware upgrade begin.
I have had to try this 2 or three times sometimes, but it has worked for me a few times now as I have been learning
I have seen this method used in an adapter with a 'reset' button, which mine does not have. If yours does, you may not have to remove the XBEE chip.