After XBee pro 900 firmware update, can't establish link

I am using XBee Pro 900’s to communicate with a uav and have had it working for a year with no issues. I upgraded the firmware to 1061 from 1021 to try to solve an issue. Now, using the same settings as before, I can not re-establish communication to the uav. I have a 2nd set of XBees with the old firmware so I just copied all the settings from those to the new ones. I can also swap out the old ones and the communication is fine. With the new version firmware xbees, they are communicating with each other it seems. I see all the lights flashing when I fire up software that uses the Xbee port, and if I interrupt the dout on the one on the uav (I have the dout connection on the xbee on a toggle switch), the lights stop flashing like it isn’t getting info.

Is there a new setting in the new firmware that needs to be changed from the default setting? Can someone post a step by step guide on how to test the link between 2 XBees on 2 separate computers using xctu?

FYI, I am using the explorer regulated on one end and the usb board on the other. I have read about issues on the regulated with the xbee pro and that you need to place a jumper on a certain resistor. I never had to do that and had perfect communication without that. Is it possible this firmware requires that to be done? I was under the impression that this firmware fixed that issue.

Thanks

after flasing the firmware, the baud rate is 9600