From your link how to upload a Hex file only the Xloader (from http://www.hobbytronics.co.uk/arduino-xloader
During uploading of DDS_Tracking.hex the RX- and TX LED on the UNO board were flashing a few seconds, so I suppose the HEX file is uploaded. The PIN 13 LED is continuously ON (on my DDS 9851 board this pin is connected to W_Clk). The Xloader app showed that 9550 bytes were uploaded.
Thank you for the link. That's a useful tool to have, and a lot easier than using AVRDude. It looks as if the HEX file has been successfully uploaded.
Trackgen firmware is detected by the analyser sending "TRACKGEN?" every time a comms port is selected, and waits to receive "TrackGenPresent" from the Arduino. If this is received then the box turns green, the Enable button is activated and the Trackgen version is displayed in the text box at the bottom of the controls group.
I have noticed some odd behavior with the comms system. If the Analyser is run and the comms port is selected, the Arduino does not always seem to detect in-coming comms from the analyser. If I then launch the Arduino IDE, or Visual Studio, and use the terminal window, I have no problems communicating with the Trackgen software. If I then re-launch the analyser, the comms system works, and communications is established. I'll look into this.
I suggest that you use the terminal window in the Arduino IDE initially. This will allow you to confirm that the firmware is installed and running, and will allow you to edit the pin numbers. There is a section at the end of the instruction manual that covers the command set you can use to run Trackgen.
The pin edit buttons will have no effect as the pin numbers are sent directly to the Arduino when the Apply button is pressed. The numbers are displayed for your information only. If there is no comms established, then the pin number updates will not take affect, although they are stored in the settings INI file. If you edit the INI file directly, then the displayed pin numbers will show the edited number, but they will not be sent to the Arduino unless the Apply button is pressed. If any changes are made in the options dialogue, such a colours, or language, the Apply button will be enabled. Every time the Apply button is pressed, the new settings are saved to the INI file, and the pin numbers are sent to the Arduino, even if none of them have been changed. Pressing the Get Pins button will cause the Arduino to send a list of the current pin settings, and these will displayed in the box at the bottom of the Tracking generator control group.
There is a problem with the pin edit boxes. If you clear the box, you will get an exception error. The underscore lines are placeholders provided by the control. As long as a number, even if it's a single digit is entered, then you should not get an exception error. This problem will be fixed in the next release.
As a general note, in the Tracking generator control group, the Step-KHz control does not allow values smaller than 0.1KHz per step to be entered. This will be changed for the next release.
If you are still having problems after trying communicating directly by using the Arduino IDE, please let me know.