I recently migrated a circuit from a breadboard to a homemade shield to plug into my Yun. I was using a large 5V supply to power my breadboard, and made the incorrect assumption that the 5V pin on my Yun would actually output 5V.
Well, after I built the shield and installed it on my Yun the results were NOT as expected! I spun my wheels trying to figure out why my circuit was working PERFECTLY before but was not working nearly as well when powered by the Yun.
As it turns out, the 5V output is more like 4.4V! That is CRAZY low for a pin labeled "5V". My shield draws a peak of 30mA. I don't know what the 5V pin is rated for but surely it should be okay with 30mA? I am powering the Yun with a micro USB cell phone charger at 5.1V. Well, now I had a decision to make: do some recalculation, reconstruction, based on the new findings, or power the Yun or shield through a different manner. I chose to deal with the 4.4V and make some modifications, but I am still not getting the performance I had previously using an actual 5V supply.
A search of this forum shows a number of other people have the same problem. So disappointing!