I have two Uno's (master and slave), separately powered ...
When you say that, do you mean one of them is unpowered? Or, this happens after you disconnect the power?
I just connected together two Unos and did not observe this, but perhaps the duty cycle on the pin is important? As CrossRoads says, this is probably going outside specifications. For example, the noise from the "power" supply, being interrupted, may cause unwanted behaviour.