Accessing onboard TX/RX leds with 12V Power Source

I have recently been playing with the usart0 on my UNO R3s (following the Atmega328 datasheet ) and am finding that I lose the onboard TX and RX leds in varying power circumstances. I'm booting and loading sketches onto two UNOs via USB from my Windows PC, then rotating one to an alternate power supply so they can communicate (via the 2x TXtoRX pins and a common GND). The communication part works just as expected in all circumstances.

However, when I rotate one to the USB Host of my Beaglebone Black (powered by 5V 2A wall supply and just used as a USB power source) the leds still blink but don't flash so much as stay on for about a half second then turn off, repeating as expected, just sluggishly. I was concerned at first that this might be a serious power issue and could be hurting the board. Is this something I should be concerned about?

Also, after seeing this I decided to try a different power supply. Now I see that if I move either board from the Windows USB and then back, the RX/TX leds won't blink again until I re-attach to the COM port (with Putty in this case). Oddly, this is not the case with the Beagle which continues to blink the leds sluggishly... Also, if I move either board to a 12V wall power source, again the RX/TX leds don't blink at all.

I'm thinking this all has to do with the 16U2 and how the power travels from the USB source through it to the rest of the board and how these leds appear to be powered by this chip, but now I am thinking I must be missing something because if I want to use serial comms between boards that aren't using USB power I will no longer have this indicator of activity...? I have tried using pins 1 and 2 as OUTPUTs and pulsing high/low to simulate the indication but this only works with USB power, which obviously defeats the purpose.

Is there a way to access these leds while not using USB supplied power?

The Rx/Tx LEDs are driven by the USB/Serial adapter - if you are not connected to USB port, nothing is driving them, and their operation is not defined.

Thanks, that's kinda what I figured, unfortunately.

Does anyone have any thoughts on the different blink rate from the Beaglebone USB host as a power source? This is not indicative of anything harmful to the Arduino is it?