I have this exact same problem, with DVCPRO HD (1080i60), Integer (Big Endian), Timecode.
It clearly shows 2 channels by pressing CMD + J within quicktime, and the audio plays fine from QT and within AE’s project window, yet no audio preview / RAM preview / output with audio.
I am completely stumped. AE CS3 really does not like the audio channels of this footage.