Mega Pro XBee Download

I’ve been having troubles lately downloading code through XBees to the Arduino Mega Pro. I am using Windows which theoretically should work and I have modified the XBees to download code wirelessly. These units work perfectly with the Arduino Pro and download fine with no errors. The only difference I have noticed between the two boards is the silkscreen print on the top pin of the FTDI connector. On the regular Arduino Pro the top pin is labeled RTS but on the Mega Pro it is labeled DTR. I have also noticed that the DIN light on the XBee is almost always lit. What I am wondering is if the DTR on the Mega pro is connected to the DIN pin on the XBee and it is not the same as the RTS pin and so whenever data is ready to be transmitted it lights up the DIN pin on the XBee.

Any suggestions?

Thanks!