I have connected a Serial to USB converter to a Xbee Series 2. Its not able to write configuration to it from XCTU

I have connected the VCC, RX, TX, DTR and GND pins to the pins on USB to serial converter Silicon Labs CP210x.

I am able to read the Xbee , update its firmware to Xbee End Device API. But when i try to write settings to it most of the time its not working.

At the Same time when i connect Xbee Series 1 I face no such problem.

When I checked the data sheet of Series 2 and Series 1 i found PIN 9 is DTR active high for Series 1 and DTR active low for Series 2. Could it be the problem.

Note that i am working the xbee from the 3.3 supply that it get from the usb to serial circuit using the Silicon Labs CP210x converter.

Yes that is part of it. You also need to use hardware flow control (/CTS) as an End device sleeps by nature and will before you can start writing the settings to it.