Originally Posted by thp

headphoned sends a "pause" signal via D-Bus to the default media player (and some others, if available). At least in my tests when the media player was running, sending a "pause" signal twice does not result in pause/unpause, but rather pause/pause (meaning that the signal does not seem to "toggle" the pause state).

This would suggest that a behaviour like this cannot come from headphoned. Feel free to try to reproduce this bug (basically by restarting your device, waiting until everything has loaded and then plugging in the headphones - the Media Player widget on your desktop might help check out the situation). If you can reliably reproduce this bug, try uninstalling headphoned and see if it still happens.