Why does music come out muddled and echoing in alarm mode when the iPhone is connected to the Bose SoundDock lll?

There is a very unique problem with the iPhone 5 and iPad mini when connected to the Bose SoundDock III.

In normal music playback, music sounds great coming out of the Bose SoundDock, but, when a song is chosen for the Apple Alarm App and turns on when the alarm goes off, the music sounds terrible. It reverberates, echoes, is muddled, sounds messy.

What is so odd about this is the same sound coming out of a speaker-device connected to the phone's headphone jack sounds perfect, and as intended.

It only has this issue when it is in alarm mode and it's connected via the lighting port connector.

Is this an Apple software glitch that wasn't researched fully or a manufacturing defect on the Bose end?

I've tried a couple Bose systems so it isn't peculiar to one SoundDock.

What are your thoughts?