I have been working with my Arduino Yun for the past few days. However, I recently ran into the issue where the Arduino GUI can no longer identify the Port for my Yun over Wi-Fi. Around the same time, the RX LED on the Arduino Yun has begun remaining constantly lit from the moment the board is turned on (even before the USB light turns on to signify that the board is running). I tried resetting the board by both holding down the WLAN button for 30 seconds and by connecting locally with it and having it reload the boot image that I provided. But I am still finding that the moment I turn the Arduino Yun on, the "ON" and "RX" LED's turn on at the same time. -- I also just tried to turn on my Arduino Yun without the SD card and yet the RX light is still on.
I am using Windows 10 + Arduino's GUI for programming.
Update: I can still SSH into the Arduino YUN (despite the constantly lit RX LED) using Bash on Ubuntu on Windows. However, I am not able to use Tools>Port (on the Arduino GUI) to upload my sketch onto the Yun.
I also was able to get to access the Arduino YUN through plugging it's IP into Google Chrome, where I (first compiled the blink file) and then attempted to upload the blink.ino.with_bootloader.hex onto my YUN. However, it is still uploading and nothing appears to be happening.
After a lot of poking, I found a workaround (not really a solution to the problem described above). For the RX LED not turning off, the problem has also apparently occurred on the Arduino Leonardo, as shown in this Youtube video:
The fix would be nearly the same if I didn't have the primary issue of not being able to find the correct port for my Arduino YUN. (In the end, while he runs avrdude he also holds down the 32U4 processor reset button and after the avrdude finishes, he releases -- at the end of this process the RX LED shuts off -- I did the same thing and it worked)
For the primary issue of not being able to select the port, I found a workaround using Bash on Ubuntu on Windows (which is the new Bash for Windows, in effect). The compiled .hex file can be scp'd from your computer to the Arduino YUN (while your root on bash is still your computer). Then, by SSH'ing to your computer you can merge the file with the bootloader and then run avrdude (by holding the 32U4 reset button during this step you can get your RX LED to turn off if it is stuck HIGH). After running avrdude, your Arduino YUN will begin running your sketch.
Here is where I found this workaround:
If you're unfamiliar with Bash on Ubuntu on Windows, it can be kind of challenging to find your documents and here is a little help for that:
You can get Bash on Ubuntu on Windows by following these steps (I found it incredibly useful):