Hi,
I have determined, at least in my case, it is not a wall wart or power issue.
I found that I got this issue every time I tried to upload a sketch larger than about 30700 bytes. I don't know the reason, but above that rough value the YUN can run the sketch, but can't reset and run the sketch. I have removed functionality (LCD) from my sketch so it is small enough to avoid these issues. Removing the bootloader and using the USBTinyISP still gets me an extra ~2000-3000 bytes so its worth it, despite the fact that I can't get a full 32000 bytes.
Nate