(Sorry for the delay - I asked one of the Xbee field engineers to look at this - here is his response.)
I have looked at this and do not believe this is a bug.
The difficulty is in making sure the command actually was sent by queue and not applied directly. For example, if the OTA command is sent without the Apply Changes option bit set, and the command is then read back via an OTA request, the request will indicate that the parameter has been set, even though the command change has not yet been applied. If the remote radio is instead Read using the XCTU, the last operation of the Read function is to send the AC command.
If you send the remote AT command and then check the remote module using the API command ID 0x09, it will read correctly, meaning the command will not have yet been applied.
If you send the remote AT command and then check the remote module using the API command ID 0x09, it will read correctly, meaning the command will not have yet been applied.
That’s the point! I checked the values via X-CTU, this caused the ‘error’.